Tai Lieu Chat Luong Amino Acids in Higher Plants Amino Acids in Higher Plants Edited by J.P.F D’Mello Formerly of SAC, University of Edinburgh King’s Buildings Campus, Edinburgh, UK CABI is a trading name of CAB International CABI 38 Chauncy Street Suite 1002 Boston, MA 02111 USA CABI Nosworthy Way Wallingford Oxfordshire OX10 8DE UK Tel: +44 (0)1491 832111 Fax: +44 (0)1491 833508 E-mail: info@cabi.org Website: www.cabi.org Tel: +1 800 552 3083 (toll free) E-mail: cabi-nao@cabi.org © CAB International 2015 All rights reserved No part of this publication may be reproduced in any form or by any means, electronically, mechanically, by photocopying, recording or otherwise, without the prior permission of the copyright owners A catalogue record for this book is available from the British Library, London, UK Library of Congress Cataloging-in-Publication Data Amino acids in higher plants / edited by J.P.F D’Mello   pages cm   Includes bibliographical references and index   ISBN 978-1-78064-263-5 (alk paper)   1.  Amino acids 2.  Plants Metabolism.  I D’Mello, J.P Felix   QK898.A5A56 2015  572′.65 dc23 2014033212 ISBN-13: 978 78064 263 Commissioning editor: Rachel Cutts Assistant editor: Alexandra Lainsbury Production editor: James Bishop Typeset by SPi, Pondicherry, India Printed and bound in the UK by CPI Group (UK) Ltd, Croydon, CR0 4YY Contents Contributors xix Preface xxiii Glossary xxvii PART I  ENZYMES AND METABOLISM 1  Glutamate Dehydrogenase G.O Osuji and W.C Madu 1.1 Abstract 1.2 Introduction 1.3  Glutamate Dehydrogenase Structure and Localization 1.4  Control Plants and Control Glutamate Dehydrogenase 1.5  Availability of Ammonium Ions 1.5.1  Ammonium ion contents of experimental tissues and plants 1.5.2  Glutamate deamination in mitochondria 1.6  Glutamate Dehydrogenase-Linked Schiff Base Amination Complex 1.6.1  Pesticide treatment and ammonium ion fertilization 1.6.2 Pesticide treatment, ammonium ion fertilization and protein contents 1.7 Protect the Glutamine Synthetase-Glutamate Synthase Cycle in Glutamate Dehydrogenase Research 1.8  Molecular Biology of Glutamate Dehydrogenase 1.8.1 The supply of a-ketoglutarate from the citric acid cycle to glutamate dehydrogenase and glutamate synthase 1.8.2  Aminating and deaminating activities 16 1.8.3  Amination-based crop yield doubling biotechnology 19 1.8.4  The aminating cassette of glutamate dehydrogenase isoenzymes 19 1.9  Food Security 20 1.10 Conclusions 23 Acknowledgements24 References24 v vi Contents 2  Alanine Aminotransferase: Amino Acid Metabolism in Higher Plants A Raychaudhuri 30 2.1 Abstract 30 2.2 Introduction 30 2.3  Structure and Functions of Alanine 31 2.3.1  Structure of alanine 31 2.3.2  Functions of alanine 31 2.4  Alanine Metabolism 32 2.4.1  Alanine metabolism by alanine aminotransferase 33 2.5  Specific Cellular and Sub-cellular Functions of Alanine Aminotransferase33 2.5.1  Homologues and tissue localization 34 2.5.2  Sub-cellular localization 35 2.6  A Phylogenetic Analysis of Alanine Aminotransferase 35 2.7  Purification of Alanine Aminotransferase 36 2.8  Protein Characterization of Alanine Aminotransferase 36 2.8.1  Subunits and substrate specificities 36 2.8.2  Kinetics and reaction mechanism 38 2.8.3  Inhibitors of the enzyme 43 2.8.4  Crystal structure 44 2.9  Diverse Roles of Alanine Aminotransferase in Plants 45 2.9.1  Roles in metabolism 45 2.9.1.1  Roles in carbon metabolism 45 2.9.1.2  Roles in photorespiration 47 2.9.1.3  Role in nitrogen use efficiency 48 2.9.2  Role in stress biology 48 2.9.2.1  Roles in hypoxia 49 2.9.2.2  Other abiotic and biotic stresses 50 2.10 Conclusions 50 References52 3  Aspartate Aminotransferase C.D Leasure and Z-H He 3.1 Abstract 3.2 Introduction 3.3  The Vitamin B6 Cofactor 3.4  Enzyme Function 3.4.1  The reaction mechanism 3.4.2  Enzyme properties 3.5  Enzyme Structure 3.5.1 K258 3.5.2 R292* 3.5.3 R386 3.5.4 D222 3.5.5 Y225 3.6  Enzyme Genetics 3.7  The Enzyme during Plant Development 3.8  The Role of Aspartate in Plants 3.8.1 C4 metabolism 3.9  Other Roles of Aspartate Aminotransferase 3.9.1 Moonlighting 3.9.2  Genetic engineering with aspartate aminotransferases 57 57 57 58 58 60 61 61 61 61 61 62 62 62 63 63 64 64 64 64 Contents vii 3.10  Future Research 65 3.11 Conclusions 65 References65 4  Tyrosine Aminotransferase A.O Hudson 68 4.1 Abstract 68 4.2 Introduction 68 4.2.1  Aminotransferases: a brief introduction 68 4.2.2  A brief history of aminotransferase activity in plants 69 4.2.3 Oligomeric state, cofactor requirement and mechanism of action of action of aminotransferases 69 4.3  Aminotransferases from the Model Organism Arabidopsis thaliana70 4.4  The Anabolism of Tyrosine and Phenylalanine in Plants and Bacteria 71 4.4.1  The anabolism of tyrosine and phenylalanine in bacteria 71 4.4.2 A second pathway for the synthesis of tyrosine and phenylalanine in plants 73 4.5 Properties of Tyrosine Aminotransferase Annotated by the Locus Tag At5g36160 from Arabidopsis thaliana74 4.5.1  Kinetic and physical properties 74 4.5.2  Substrate specificity 76 4.5.3  In vivo analysis of tyrosine aminotransferase 76 4.6  The Role of Tyrosine Aminotransferase in Plants 77 4.7 Conclusions 79 Acknowledgement79 References79 5  An insight Into the Role and Regulation of Glutamine Synthetase in Plants C Sengupta-Gopalan and J.L Ortega 82 5.1 Abstract 82 5.2 Introduction 82 5.3  Classification of Glutamine Synthetase 83 5.4  Glutamine Synthetase in Plants 83 5.4.1  Chloroplastic glutamine synthetase 84 5.4.2  Cytosolic glutamine synthetase 84 5.5  Modulation of Glutamine Synthetase Expression in Transgenic Plants 86 5.6  Regulation of Glutamine Synthetase Gene Expression in Plants 88 5.6.1  Transcriptional regulation 88 5.6.2  Post-transcriptional regulation 89 5.6.3  Translational regulation 91 5.6.4  Post-translational regulation 91 5.7  Concluding Remarks 93 Acknowledgements94 References94 6  Asparagine Synthetase S.M.G Duff 6.1 Abstract 6.2 Introduction: the Role of Asparagine and Asparagine Synthetase in Nitrogen Metabolism 6.3  Asparagine: History, Chemical Properties and Role in Plants 100 100 100 101 viii Contents 6.4 Asparagine Synthetase: an Early History of Research in Humans, Microbes and Plants 102 6.5  The Occurrence of Asparagine Synthetase in Nature 104 6.6  The Expression and Function of Asparagine Synthetase in Plants 105 6.6.1  Nutritional and mineral deficiency 105 6.6.2  Seed germination 105 6.6.3  Light signalling 106 6.6.4  Developmental stage and tissue specificity 106 6.6.5  Environmental stress and carbohydrate depletion 107 6.6.6  Senescence and nitrogen remobilization 108 6.6.7  Seed maturation 108 6.6.8 Photorespiration 109 6.6.9  Nitrogen signalling and glutamine:asparagine ratio 109 6.6.10 Asparagine: a nitrogen carrier, storage compound, detoxification mechanism and signal 110 6.7 Phylogeny, Subunit Structure and Enzymatic Activity of Asparagine Synthetase 110 6.7.1 Phylogeny 110 6.7.2  Subunit structure 112 6.7.3  The enzymatic activities of asparagine synthesis 112 6.8 Kinetics, Reaction Mechanism and Crystal Structure of B-type Asparagine Synthetases 112 6.8.1  Kinetics of plant asparagine synthetase 112 6.8.2 The crystal structure and reaction mechanism of asparagine synthetase 114 6.9  Other Routes of Asparagine Synthesis in Plants 116 6.10  Asparagine Catabolism 116 6.11  Asparagine Synthetase and Agriculture 117 6.11.1  Seed protein content and crop yield 117 6.11.2  The impact of plant nutrition 118 6.11.3  Metabolic engineering and transgenic studies 118 6.12 Conclusions 120 Acknowledgements120 References120 7  Glutamate Decarboxylase J.J Molina-Rueda, A Garrido-Aranda and F Gallardo 129 7.1 Abstract 129 7.2 Introduction 129 7.3  Characteristics of Glutamate Decarboxylase in Plants 130 7.4  Glutamate Decarboxylase Gene Family 131 7.5  Expression of Glutamate Decarboxylase Genes 131 7.6  g-Aminobutyric Acid Synthesis and its Metabolic Context 135 7.6.1 The g-aminobutyric acid shunt pathway and stress 135 7.6.2 Alternative sources of g-aminobutyric acid in plant tissues and transport 137 7.7 Classical and Recent Evidence Supporting the Functions of Glutamate Decarboxylase and g-Aminobutyric Acid 137 7.8  Future Research 139 Acknowledgement139 References139 Contents ix 8  l-Arginine-Dependent Nitric Oxide Synthase Activity142 F.J Corpas, L.A del Río, J.M Palma and J.B Barroso 8.1 Abstract 142 8.2 Introduction 142 8.3  Arginine Catabolism in Plants: Urea, Polyamines and Nitric Oxide 143 8.3.1  Urea metabolism 144 8.3.2  l-Arginine modulates polyamine and nitric oxide biosynthesis 144 8.3.3  Arginine and nitric oxide synthesis in higher plants 145 8.4 Modulation of l-arginine-dependent Nitric Oxide Synthase Activity During Plant Development and Under Stress Conditions 147 8.4.1  Nitric oxide synthase activity during plant development 147 8.4.2  Nitric oxide synthase activity in plants under stress conditions 149 8.5 A Genetic Engineering Approach to Study of the Relevance of Nitric Oxide Synthase Activity in Plants 150 8.6 Conclusions 150 Acknowledgements151 References151 9 Ornithine: At the Crossroads of Multiple Paths to Amino Acids and Polyamines R Majumdar, R Minocha and S.C Minocha 156 9.1 Abstract 156 9.2 Introduction 156 9.3  Ornithine Biosynthesis and Utilization 158 9.4  Cellular Contents 159 9.5  Mutants of Ornithine Biosynthesis 160 9.6 Genetic Manipulation of Ornithine Metabolism and its Impact on Amino Acids and Other Related Compounds 164 9.7  Ornithine Biosynthesis and Functions in Animals 168 9.8  Exogenous Supply of d- and l-Ornithine169 9.9 Modelling of Ornithine Metabolism and Associated Flux: Ornithine as a Regulatory Molecule 170 9.10 Conclusions 171 Acknowledgements172 References172 10 Polyamines in Plants: Biosynthesis From Arginine, and Metabolic, Physiological and Stress-response Roles A.K Mattoo, T Fatima, R.K Upadhyay and A.K Handa 177 10.1 Abstract 177 10.2 Introduction 177 10.3  Substrates and Enzymes Catalysing 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acetyltransferase  195–207 serotonin N-acetyltransferase (SNAT)  400, 402–403, 406 acid hydrolysis  482–483, 488 acivicin 450, 451 ackee fruit (Blighia sapida)  512, 520, 521–522 acrylamide  118, 487, 488 acute toxicity testing  471, 518 additive interactions  522, 557, 559 adenosine 5'-phosphosulfate reductase (APR)  206, 207–209, 221, 225 S-adenosylmethionine (SAM) homeostatic regulation in cells  183 inhibition of aspartate kinase  236 role in metabolic pathways  180, 182, 545 S-adenosylmethionine decarboxylase (SAMDC) 180–181 ADME studies (toxicology)  470 advanced glycation end-products (AGEs)  566 agmatine  144, 178–179 agmatine iminohydrolase (AIH)  179–180 alanine (Ala) accumulation in oxygen deficiency  268–270, 269 functions in plants  31–32 metabolism  32, 32–33 structure and natural occurrence  31, 31 alanine aminotransferase (AlaAT) enzyme characterization  30 inhibitors 43, 43 kinetics and reaction mechanism  38, 41–42, 42 molecular structure  44, 44–45 reaction catalysed  33, 33 subunit structures and substrates  36–38, 39–40 localization in cells and tissues diversity of specific activities  33–34 homologues in different tissues  34–35 sub-cellular locations and activities  35 phylogenetic analysis  35–36, 37 purification 36, 38 roles in plant biology  30–31, 45, 51 carbon and nitrogen metabolism  45–48, 46 stress responses  48–50, 268–269, 269 alanine:glyoxylate aminotransferase (AGT)  35 albizziin 450–451, 451 585 586 Index alcohol dehydrogenase (ADH)  267 algae, carbon/nitrogen metabolism  282–283, 286–287 alkali hydrolysis  483–485, 484, 486 alkaloids 167 allelopathy  442, 443, 454, 514 amine oxidases, copper-containing (CuAO)  145, 183 amino acid permease (AAP) transporters  320, 329 amino acid–polyamine–organocation superfamily see APC transporters amino acids analogues  448, 450, 454, 510, 510–511 analytical methods composition of plant products  488–492 data presentation  488 free amino acid content  487 sample preparation  482 techniques  481–482, 482–487 biosynthesis connection with glucosinolate ­metabolism  440–441 role of ornithine  157, 159 in stress  262–263, 264 d- and l- isomers  491–492, 552–553 export dynamics  298–307 metabolic availability (in foods)  499–503 summary of roles in plants  538–541 b-aminobutyric acid (BABA)  515, 518, 525–527, 563 g-aminobutyric acid see GABA S-aminoethyl-l-cysteine (AEC)  239, 454, 454 aminomethylphosphonic acid (AMPA) levels in plants  463–466, 467 microbiological product in soil  467–468, 469, 470 aminotransferases in Arabidopsis genome  51, 70–71, 71, 72 catalytic properties  32, 68–69, 69 inhibitors 43, 449, 449–450, 454 metabolic roles in plants and animals  69, 550, 552 specific enzymes alanine aminotransferase  33–51 aspartate aminotransferase  57–65 tyrosine aminotransferase  71–79 structures and action mechanisms  69–70, 70 ammonium ions (NH4+) assimilation green microalgae  282–283 vascular plants  84, 283, 284, 318 metabolic availability  4–5 produced and oxidised by soil microbes  317–318 released by photorespiration  109, 278 amplified fragment length polymorphisms (AFLPs) 210 antagonistic interactions  514, 518, 556, 558, 558 anthranilate synthase (AnS)  86, 362, 363–364 APC transporters  137, 303–304, 304 aphid feeding, plant responses  163, 565 Arabidopsis thaliana (model organism) aminotransferase genes  51, 70–71, 71, 72 glutamate decarboxylase gene family  132 SERAT and OASTL (cysteine synthase) enzymes 222, 222 arginase  144, 512–513, 523, 542, 560 in animals  168 arginine (Arg) analogues (non-protein AAs)  144, 510, 520–521 metabolic roles  542 in defence responses  560 l-arginine catabolism in plants  143, 143–147 synthesis in urea cycle  513, 513 residues R292* and R386 in AspAT ­apoprotein  61–62 arginine decarboxylase (ADC)  164, 165, 167, 178–179 aromatic amino acids analogues (non-protein AAs)  510–511 biosynthesis and roles  71–73, 72, 73, 547–549, 548 effects of deficiency  462 ascaulitoxin aglycone  454, 455 asparaginase (Asnase)  102–103, 116–117 asparagine (Asn) biosynthesis 102, 103, 116, 116, 319 catabolism 116–117, 117 quantitative analysis  483, 487 roles in plants  100, 102, 110, 120 accumulation in abiotic stress  271 agricultural implications  117–118 N status, importance relative to ­glutamine  109, 328 structure and properties  101, 101–102 asparagine synthetase (AsnS, AS) discovery and research  102–104, 120 enzyme characterization kinetics and reaction mechanism  112–114, 114, 115, 115–116 molecular structure  112, 114–115 reactions catalysed  104, 112, 113 inhibition by albizziin  450–451 metabolic engineering with transgenics  87–88, 118–120 occurrence of A and B forms  104–105 phylogeny 110, 111–112 roles in plant metabolism  101, 105–106, 107–109 expression in stress  271 tissue-specific expression  106–107 Index 587 aspartate (aspartic acid, Asp) in C4 metabolism  64 residue D222 in AspAT apoprotein  62 synthesis and roles in plants  57–58, 63–64 allosteric control of glycolysis  290 aspartate metabolic pathway  234–238, 235, 264, 270–272 aspartate aminotransferase (AspAT, AAT) enzyme structure and function reaction mechanism  60–61 structure  44, 58–59, 61–62 substrate affinities  61 transamination reaction  59, 59–60 genetic regulation expression and localization during development  63, 65 genes and gene products  62–63 genetic engineering opportunities  64 roles in plant metabolism  57–58, 65 long-chain fatty acid uptake  64 nitrogen and C4 pathways  63–64 vitamin B6 homeostatic sensing  63 aspartate kinase (AK)  236–237 aspartate semialdehyde dehydrogenase ­(ASADH)  237 aspergillomarasmine A  454, 456 ATP (adenosine triphosphate) enzyme binding sites  83, 115 production pathways  46, 50, 266, 288 requirement for asparagine synthesis  101, 102, 104, 104 used in sulphate assimilation  220, 221 ATP-binding cassette (ABC) transporters  304–305 autophagy 228–229 auxin biosynthesis endogenous auxin types  341, 348, 348–349 evolution in plants  352–354 history of research  341–342 pathways 342–348, 347, 354, 548 regulation environmental responses  350–351 genetic, mechanisms  349–350 homeostasis, role of conjugates  352, 353, 549, 554 hormonal 351–352 tissue and cellular sites  342 see also indole acetic acid availability amino acids bioavailability in foodstuffs  497–503, 566 non-protein amino acids  508 for plant stress tolerance  263 energy  93, 263, 271 metabolic availability (MA) assay  499–503 metabolic sources of NH4+ ions  4–5 nitrogen, in soils  315–318, 319 avenanthramides (Avs)  372–375, 373, 375 BABA (b-aminobutyric acid)  515, 518, 525–527, 563 barley (Hordeum spp.)  368 BCNA (b-cyanoalanine)  512, 518, 519, 524 benzoxazinones (Bxs) defence response mechanisms  371–372 glycosylation and toxicity  369–371 synthetic pathway  364–368, 365 bialaphos  449, 451, 452, 453 bioavailability of AAs in foods  497–503 biotic stress responses see allelopathy; defence responses bisavenanthramides (bisAvs), antifungal ­activity  374–375, 375 BMAA (b-N-methylamino-l-alanine)  510, 515, 521, 524 BOAA (b-N-oxalylamino-l-alanine)  510, 519, 521 branched-chain amino acids (BCAAs)  270, 545–547 aminotransferases (BCATs)  438, 546 Brassica forage toxicity  512, 519, 524, 528, 529 brassinosteroids  441, 546 C4 metabolism AlaAT as C/N metabolism shuttle  34, 45, 46 aspartate and AspAT involvement  64 Ca-binding protein kinases  267 cadaverine 167 callose deposition  372, 442, 526 calmodulin (CaM) binding domain in GAD  130, 131, 134, 134 complex, with nitric oxide synthase  145 camalexin  226, 346, 563, 564 cAMP (cyclic adenosine monophosphate)  403 canavanine metabolism 512–513, 513 detoxification 527 as potential anti-cancer drug  144 toxicity  515, 517–518, 520, 522–523 cancer therapy  394, 528–529, 569 carbamoyl phosphate synthatase (CPS)  164 carbon metabolism primary pathways in plants  278–282, 279, 284 responses to carbon depletion  107–108 responses to nitrogen supply  282–284 roles of AlaAT  45–47, 46 carcinogens 472–473 CAS (b-cyanoalanine synthase)  226–227 castor oil seed (Ricinus communis) metabolism  287 Cauliflower mosaic virus (CaMV) promoter  158, 165 cell walls phenolic polymers  377, 380 reinforced by avenanthramides  375, 376 chitin, elicitor of Avs in oat leaves  374, 376 chloroplastic glutamine synthetase (GS2)  84, 88 588 Index chorismate as aromatic AA precursor  71–73, 72, 73 secondary metabolite derivatives  374 chromatography (in AA analysis)  486, 487, 492 citrulline (Cit)  158, 164, 542–543 climate change impacts  22, 315–316, 330 cofactors, pyridoxal-5'-phosphate (active vitamin B6) as AlaAT cofactor  33, 44, 44–45 as AspAT cofactor  58, 59 competitive inhibition  452, 523 complementary DNA (cDNA), in enzyme ­characterization  74, 239, 241 cornexistin  449, 450 crop yield GDH amination-based doubling  19, 20–23, 22 genetic improvement and Asn ­metabolism  117–118 cross-talk, in signalling  351, 527, 554, 559, 563 CS26 (S-sulfocysteine synthase)  225–226 b-cyanoalanine (BCNA)  512, 518, 519, 524 b-cyanoalanine synthase (CAS, CYS-C1)  226–227 cyanogenic glucosides  369, 370, 436, 437 cycad flour toxicity  521 cycloserine  43, 44–45 CYS-C1 (b-cyanoalanine synthase)  226–227 b-cystathionase 450 cystathionine-g-synthase (CGS)  237 cysteine (Cys) biosynthesis  195–196, 199, 200, 222 cellular compartmentalization  224, 225 homeostatic regulation  222–224, 223 quantitative analysis  483, 490 roles in plants  220, 225–229, 545 l-cysteine desulfhydrase (DES)  227–229 cysteine synthase complex regulatory function  206, 222–224 structure and components  199–202, 200 see also O-acetylserine(thiol)-lyase cytosolic glutamine synthetase (GS1) 84–88 DABA (a,g-diaminobutyric acid)  519, 524 decarboxylases functions in plants and animals  550–551, 552 specific types S-adenosylmethionine decarboxylase  180–181 glutamate decarboxylase  129–139 glycine decarboxylase  543, 550–551 ornithine decarboxylase  522 tryptophan decarboxylase (TDC)  399, 401–402, 405–406 defence responses (biotic stress) categories of activity  442 hypersensitivity  150, 228 inducible responses  371–372, 374–375, 377–379 involvement of secondary compounds  549–550 modulation of nitrogen metabolism  119–120 physical responses  372, 377 and plant hormones  554, 567–568 resistance priming with BABA  526 signalling pathways  50 dehydrogenases aspartate semialdehyde dehydrogenase  237 glutamate dehydrogenase  2–20 homoserine dehydrogenase  236–237 deoxyxylulose phosphate (DXP)  58 derivatizing reagents  486, 492 DES (l-cysteine desulfhydrase)  227–229 developmental and reproductive toxicology (DART) 473–474 diamine oxidase (DAO)  171, 183 DIBOA/DIMBOA  364–366, 369 digestibility 498–499 dihydrodipicolinate synthase (DHDPS)  238–240, 453–454 dihydroxyacetone phosphate (DHAP)  286 Dof transcription factors  89 DOPA (3,4-dihydroxyphenylalanine)  401, 510–511, 517 drug/metabolite transporter family (DMT)  302–303 endocrine disruption  474 energy availability in stress  93, 263, 271 energy homeostasis  46–47, 50 environment abiotic stress factors  262–263, 560, 562–563 fate and behaviour of glyphosate  463, 466–469, 470 stress response enhancement  134, 526–527 enzymes in plants and animals, compared  550–553, 551 research on regulatory mechanisms  92, 572 salvage pathway in plants  58 substrate specificity in bacteria and plants  41 see also aminotransferases; decarboxylases; dehydrogenases; synthetases/synthases EPSPS (5-enolpyruvylshikimate-3-phosphate synthase)  456, 462, 465 ethylene (ET), biosynthetic pathway  182–183, 544, 545 inhibition by rhizobitoxine  450 evolution see phylogenetic studies fertilizers, NH4Cl treatments in GDH activity research 6–7 flavin adenine dinucleotide (FAD) cofactor  145, 343, 344 flavin mononucleotide (FMN)  145 Index 589 flavin monoxygenase (FMO)  343 flavonoids 565 food security benefits of herbicide use  461 role of GDH amination in crop yield increase  2, 19, 20–23 GABA (g-aminobutyric acid) as non-protein amino acid  510 phytotoxicity 517 roles in plant biology  129, 137–139, 525 abiotic stress tolerance  267 GABA shunt pathway in stress  49, 135–136, 136, 171 in plant–pathogen interactions  307, 554 sources and transporters  137 synthesis control by GS  85, 292 gabaculine  449, 449–450 gene chip operating software  203 genotoxins 472 germination, seeds  105–106, 164, 329 gibberellin (GA)  89 b-glucosidases  369, 370–371 glucosinolates  369, 436–443, 439, 546, 565–566 glufosinate  451, 453 glutamate (glutamic acid, Glu) homeostasis  291–292, 541 metabolic roles and pathways  541 family stress response pathway  264, 264–267 linking carbon and nitrogen metabolism  14, 14–15, 135, 136, 138 biosynthesis  2, 3, deamination 5 feedback inhibition in glycolysis  290 receptor agonists  510, 521, 524, 541, 553 in transgenic tomatoes, effect on taste  134–135 glutamate decarboxylase (GAD) biological roles  129, 137–139 in GABA shunt pathway  135–136, 136, 267 regulation expression patterns  131–134, 135 GAD gene family, phylogeny  131, 132, 133 overexpression and silencing  134–135 role of ornithine  171 structures and properties  130, 130–131, 134 glutamate dehydrogenase (GDH) catalytic activities amination, with Schiff base complex  5–7 assay design considerations  4–5, 7–8 enzyme characteristics cellular localization  isomerization response to stimuli  3–4, 6–7, molecular and active site structure  2–3 regulation in animals and plants  550, 560 roles in primary metabolism  8–16, 10, 11, 13 amination vs deamination, relative importance  16–19, 23–24 ammonia detoxification  105 research on activity in peanuts  19–20 RNA synthesis  2, 9–12 glutamate-like receptors (GLRs)  541, 553, 560 glutamate pyruvate aminotransferase (GPAT) see alanine aminotransferase glutamate semialdehyde (GSA)  266 glutamate synthase (GOGAT)  7–10, 63, 105 glutamate:glyoxylate aminotransferases (GGATs) activity regulation  34 kinetic properties  41–42, 42 in peroxisomes  35, 47 structure compared with AlaAT  30, 33, 36 glutamine (Gln) analogues, as enzyme inhibitors  450–451 quantitative analysis  483 ratio to asparagine, N status signalling  109 regulation by GDU1 (Glutamine Dumper1) 301, 305–306 synthesis and amino-N transfer  83, 319, 328 glutamine synthetase (GS) genetic regulation post-transcriptional 89–90 post-translational 91–93 transcriptional 88–89 translational 91 inhibitors 451–453, 452 involved in photorespiration  109 isoforms in plants chloroplastic GS2 84 cytosolic GS1 84–86 phylogeny 83–84 modulation in transgenic plants  86–88 reaction catalysed  63, 83, 144 structural types, in pro- and eukaryotes  83, 453 glutathione, reduced (GSH)  92, 143, 206, 207 glycine (Gly) metabolic roles  543–544 structural relationship to glyphosate  462, 470 glycine betaine (GB)  543–544, 545, 560, 562–563 glycine decarboxylase  48, 543, 550–551 glycine N-methyltransferase (GNMT)  183 glycolysis  46–47, 50, 280–282, 281 glycosylation 368–369 glycosyltransferases (GTs)  369–370 glyphosate effects and impacts  463 environmental fate  466–469, 470 herbicidal action  462 mammals/humans, health risk ­assessment  469–476, 476 plant uptake and metabolism  463–466, 467 590 Index glyphosate (continued) history of development and use  461–462 structure and properties  462, 462–463 good agricultural practices (GAP)  464–465, 475 gostatin  449, 450 gramine  365, 368 grasses (Poaceae) 364 genome components  366–368 groundwater contamination  469 GS-GOGAT cycle protection during GDH studies  7–8 reactions and enzymes  83, 102, 103, 319 role in N assimilation  108, 116, 277–278, 278 tissue localization  318 guanidination method  489–490 heat processing damage  498, 499, 501, 503 heavy metal tolerance  207, 228, 265, 560 hemiparasitic plants  324–325 herbicides  450–454, 456, 461–466, 528 herbivores induced plant responses  371–372, 374–375, 379 glucosinolate regulation  441 host–insect interactions  553, 565, 571–572 plant defences chemical (constitutive)  364, 376–377 ‘mustard oil bomb’  439, 440, 442–443 physical 377 histidine (His) biosynthesis  251–252, 256 localization and evolution  256 pathway and enzymes (HISNs)  252–256, 253 regulation  252, 256–257 properties and occurrence  251, 252 role in nickel hyperaccumulation  258 histidinol phosphate  255 homoarginine  520–521, 523 homoserine dehydrogenase (HSDH)  236–237 homoserine kinase (HK)  237–238 housekeeping genes  107 human health dietary concerns  21–22, 234, 237, 474–475, 499 drinking water quality  469, 475 effects of melatonin  391–395, 393 non-protein amino acids potential therapeutic uses  528–529 risks, in diet  520–522 nutraceutical products  169, 565–566 risk assessments for glyphosate  471–474, 475–476, 476 hydrolysis methods  482–486, 484, 486, 490–491 hydroponic solutions  443, 464 hydroxyindole O-methyltransferase (HIOMT)  400, 403–404, 407 5-hydroxytryptamine see serotonin 5-hydroxytryptophan (5-HTP)  401–402 hypersensitive response  150, 228 hypoglycins  511, 520, 524 hypoxia roles of AlaAT  35, 46–47, 49–50, 268–269 stress response pathways  267–270, 269 IAAO (indicator amino acid oxidation) technique  499, 499–500, 502–503 IAM (indole-3-acetamide) pathway  346–347 IAOx (indole-3-acetaldoxime) pathway  346 ileal digestibility  490, 498–499, 501, 503 imidazole acetol-phosphate (IAP)  254–255 imidazole glycerol phosphate (ImGP)  254 indicator amino acid oxidation (IAAO) technique  499, 499–500, 502–503 indolamine 2,3-dioxygenase (IDO)  414 indole-3-butyric acid (IBA)  348, 349 indole acetic acid (IAA) compared with melatonin  413 discovery 341 role of glutamine in synthesis  86 structure 348 see also auxin biosynthesis indole glucosinolate  346, 364, 438 indolic pathway, melatonin catabolism  407, 408 indospicine  519, 521, 523 inositol monophosphatase enzymes (IMPs)  255 insecticidal activity  517–518, 528 interactions see molecular interactions; pathogens, interactions with plants internal standards  488 inulin 119 ionotropic glutamate receptors (iGluR)  541, 553 IPA (indole-3-pyruvate) pathway  343–345, 344, 345, 354 isoleucine (Ile)  272, 545–546 isothiocyanates 440, 442, 442–443, 566 jack bean (Canavalia ensiformis), toxicity  512, 518, 528 jasmonic acid (jasmonate, JA) inducing serotonin accumulation  379 isoleucine conjugate  547, 553 signal transduction in insect injury  565, 571 synergistic and antagonistic interactions  556, 558 a-ketoglutarate (a-KG) as amination substrate of GDH  2, 7, 12, 14 providing C backbone for N compounds  278 Index 591 regulation of GS activity  88 roles in AlaAT activity  32, 33, 42 kwashiorkor 21–22 kynuric pathway, melatonin catabolism  407–409, 408 lactate dehydrogenase (LDH)  267 LCMS (liquid chromatography–mass spectrometry) 487 least-squares non-linear regression  484, 484–486, 485, 486, 491 legumes methionine content  237 non-protein amino acids  508, 511–512, 515 symbiotic nitrogen-fixing bacteroids  306–307, 323–324, 546, 559 Leucaena leucocephala, toxicity  514, 515, 520, 521, 527–528 leucine (Leu) Leu-zipper proteins  546, 567 role in stress responses  270 leucine-rich repeat receptor kinase (LRR-RK)  546, 554 light regulation of gene expression  88 signalling responses  106, 568 livestock feedstuffs adverse effects of non-protein AAs  509, 512, 518–520, 527–528 digestibility 498–499 protein quallity  566 long-chain fatty acid uptake  64 low oxygen escape syndrome  49 lysine (Lys) analogues  239, 454, 454 dietary requirements and supply  234, 245, 566 metabolic availability assessment  501–502, 502 Maillard derivatives  488, 489 metabolism biosynthesis 234–235, 235, 238–240, 453–454 catabolism, degradation pathway  235, 240–243, 272 regulation and manipulation  235–236, 243–245, 244 quantitative determination methods  489–490 residue K258 in AspAT apoprotein  60, 61 lysine a-ketoglutarate reductase (LKR, LOR)  240–243, 272 Maillard reactions  488, 489, 498 major facilitator superfamily (MFS) transporters  305 mangotoxin 453 mass spectrometry  486–487 coupled with gas chromatography (GC-MS)  343, 396 inductively coupled plasma (ICP-) MS  210 maximum residue levels (MRLs)  475 melatonin biological functions roles and beneficial effects in animals  391–394, 392, 393 roles in higher plants  410–415, 411 biosynthetic pathway  396, 398, 404 enzymes and regulation  396, 399–400, 401–407 catabolism 407–409, 408 characteristics  390, 394–395 discovery and natural occurrence  391, 395–396, 397–398 detection and quantification in plants 409–410 metabolic availability (MA) assay  499–503 metabolic mimicry  524 metabolism amino acids of central importance  541, 569–570 comparative (animals and plants)  550–553, 551, 568 primary 278–282, 279, 284, 540 research engineering, with transgenics  118–120, 290–292, 364 methods and approaches  272–273 secondary  363–364, 508–509, 549–550 see also stress metabolism methionine (Met) content in legumes  237 quantitative analysis  483, 490, 490–491 role in ethylene biosynthesis  450, 544, 545 synthesis and degradation  544–545 methionine cycle  180, 182 methionine sulfoximine  107, 452, 452 S-methyl-5'-thioadenosine (MTA)  180 methyl jasmonate (MeJA)  163, 167, 556 b-N-methylamino-l-alanine (BMAA)  510, 515, 521, 524 S-methylcysteine sulfoxide (SMCO)  513, 519, 523–524, 527, 528 microorganisms degradation of glyphosate  467–468, 470 effects of non-protein AAs on ecology  508, 515 fungal spore germination  375, 375 phytotoxic secondary compounds  499, 449–450 responses to root exudates  306 in rumen of livestock  513, 514, 520, 527–528 in soil, competition with roots  318, 320–321 microwave hydrolysis  483 592 Index mimosine metabolism  513–514, 524 detoxification 527–528 potential uses  528, 529 toxicity  515, 517, 520, 521 mitochondria glycine metabolism  48, 543 used in GDH activity assays  mitogen-activated protein kinases (MAPK)  267 molecular interactions electrostatic 185 integration in complex systems  545, 558–559 types of interaction  554, 556, 557–558, 558 molecular weights  488 Moore and Stein procedure  481–482 ‘mustard oil bomb’  439, 440, 442–443 mycorrhizae 321–323 myrosinase  439, 440, 442 neurotoxins  474, 487, 512, 524 nickel, hyperaccumulation in plants  258 nitrate (NO3-) in post-transcriptional regulation  90 resupply to N-starved plants  283–284 transported in xylem sap  326 uptake by roots  87, 138, 318 nitric oxide (NO) effects of non-protein AAs on production  523, 525 metabolic roles  143, 147, 149–150, 159 signalling in N-fixation  92 physiological sources  142, 145–147, 542, 543 nitric oxide synthase (NOS) activity regulation during development  147–149 in stress conditions  149–150 enzyme structure and activity  145–147, 146, 148 genetic engineering for stress resistance  150 nitrogen cycle (in ecosystems)  315–316, 330 nitrogen-fixing bacteria  306–307, 323–324 nitrogen metabolism assimilation  82–83, 277–282, 317–319 role of GS  93 remobilization in senescence  108, 144 resupply after starvation  90, 282–284 storage and transport within plants  31, 263, 298–302 role of l-arginine  143, 328 transpiration stream loading  325–328, 327 use of asparagine  100, 102, 110 xylem–phloem exchange  328–329 supply signalling, Asn:Gln ratio  109 uptake of organic (amino-) nitrogen  316–317, 319–325 see also urea cycle nitrogen use efficiency  48, 86, 117–118 S-nitrosoglutathione (GSNO)  143 NLP1 enzyme (putrescine synthesis)  178, 180 NMDA-like receptors  543, 556 nodulin-26 93 non-protein amino acids classification criteria  509–511, 510 distribution and concentrations  511, 511–512 metabolic roles  156, 509, 525–527 metabolism of specific types  512–514 potential applications  528–529, 530–531 toxicity  508–509, 514, 522–525 adverse effects on higher animals  518–520 anti-microbial activity  515 detoxification 527–528 human health risks  520–522 insecticidal activity  517–518 phytotoxicity  448, 451, 515–517, 516 nuclear magnetic resonance (NMR) analysis  184, 487 nucleotide metabolism  256, 257 nutraceutical supplements  169, 565–566 nutrition (human/animal diet) arginine supply and demand  168 bioavailability of amino acids  497–503, 566 dietary fibre importance  499, 503 effects of food processing on amino acids  488–489, 490, 491–492 lysine deficiency, cereals  234 methionine deficiency, legumes  237 protein–energy inadequacy (kwashirokor)  21–22 toxicology related to exposure  474–475, 514 nutrition (plant minerals) deficiencies and asparagine levels  105, 118 imbalances, Orn role in stress tolerance  167–168 nitrogen import/export physiology  298–300, 315–325 sulfate assimilation  195–196, 196, 220–222, 221 OAS (/OASTL) see O-acetylserine (/OAS(thiol)-lyase) oats (Avena sativa)  372–375 ornithine (Orn) biosynthesis and metabolism  156–158 in animals  168–169 flux modelling  170–172 in plants  157, 158–159 content, in cells  159–160, 160, 161–162 effects of exogenous supply  169–170 genetic regulation of pathways mutant studies  160, 163–164 transgenic modulation impacts  164–168, 166, 542 Index 593 ornithine aminotransferase (OAT)  164–165, 168, 266, 542 ornithine cyclodeaminase (OCD)  167 ornithine decarboxylase (ODC)  164, 165–167, 168, 178, 522 ornithine transcarbamoylase (OTC, OCTase)  164, 453 osmotic stress protection  168, 265–267, 272 oxaloacetate (OAA)  278–280 b-N-oxalylamino-l-alanine (BOAA)  510, 519, 521 oxetin 451, 452 2-oxoglutarate (2-OG) see a-ketoglutarate oxygen deficiency see hypoxia ozone chemiluminescence method  146–147, 149 P5C (Δ1-pyrroline-5-carboxylate) enzymes  266 Parkinson’s disease complex (ALS/PDC)  474, 521 pathogens, interactions with plants amino acid signalling  307 induced plant responses  371–372, 374–375, 377–379 glucosinolate metabolism  441, 442–443 plant chemical defence  364 resistance priming  526, 571 performic acid oxidation  482, 483 peribacteroid membrane (PBM)  323–324 pesticides degradation pathways  467 soil organic matter adsorption  468, 469 toxicology  472, 474 treatments in GDH activity research  6–7, usage regulation and approval  473, 475 phaseolotoxin 453, 453 phenylacetic acid (PAA)  348 phenylalanine (Phe) biosynthesis in bacteria  71–73, 72 in plants  73, 73, 547 interaction with phytotoxins  454 photodegradation 454 phenylalanine ammonia lyase (PAL)  524, 547, 569 phenylpropanoid pathway  77–78, 78, 79, 374, 524 release and re-assimilation of ammonia  85 3-phenylpropionic acid (PPA)  348 phloem exchange of amino-N with xylem  328–329 S-cells and glucosinolates  439, 440 phosphinothricin 451, 452, 453 3'-phosphoadenosine 5'-phosphosulfate (PAPS)  196, 221 phosphoenolpyruvate (PEP)  280–282, 281, 292 phosphoenolpyruvate carboxykinase (PEPCK)  64 phosphoenolpyruvate carboxylase (PEPC) metabolic engineering  290–291 structures and activity  279, 284–288, 285, 289–290 O-phosphohomoserine (OPH)  237–238 5-phosphoribosyl-3-pyrophosphate (PRPP)  252, 256, 257 photodegradation glyphosate 466–467 phenylalanine 454 protective mechanisms in high light S-sulfocysteine synthase  226 vitamin B6 58 photorespiration ammonium recycling  86, 109, 278, 451 role of AlaAT  35, 47–48 phylogenetic studies alanine aminotransferase  35–36, 37 asparagine synthetase  110, 111–112 components of cysteine synthase complex 222, 223 glutamate decarboxylase  131, 133 glutamine synthetase isoforms  83–84 Trp pathway defensive metabolism  381 gene cluster evolution, Bx pathway  366–368 glucosinolate biosynthesis  436, 437 serotonin induced by infection  378–379, 379 phytoalexins  150, 372–375, 570 phytochrome B  350 phytotoxins investigation strategies  449 types and actions  448–456 glucosinolate derivatives  442–443 glyphosate 462–466 non-protein amino acids  515–517, 516 PII proteins  158, 160 ping-pong reaction mechanisms of aminotransferases  42, 59, 59, 70 histidinol oxidation  256 plant products (used by humans)  565–566, 568–569 AA composition determination  488–492 uses of melatonin  415–416 polyamine oxidases (PAO)  183–184 polyamines biosynthesis from arginine  143, 144–145, 164 pathways and enzymes  178–182, 179, 182 deamination, and ROS signalling  145, 183–184 homeostatic regulation Orn pathway  159, 165–168 SAM substrate flux  180, 182–183 research questions  188 roles in plants growth and development processes  185–186 metabolic regulation  184, 184–185 responses to abiotic stress  186, 187, 263 types and occurrence in plants  177–178 see also APC transporters 594 Index post-transcriptional regulation  87, 89–90 post-translational regulation  91–93, 185, 242 potentiation mechanisms  526–527 PRFAR 254 programmed cell death  138–139, 150, 228 proline (Pro) accumulation in stress  168, 264–265, 560 regulation 266–267 primary and secondary metabolic roles  541–542 proline dehydrogenase (ProDH)  266 proline-rich proteins  560 protoxins  449, 451–453 PSorn (OCTase inhibitor)  453, 453 putrescine (Put) biosynthesis 178–180, 179 and ornithine metabolism  158, 165, 166 pyridoxal-5'-phosphate (PLP, active vitamin B6) active site reaction mechanism  60, 70 as cofactor alanine aminotransferase  33, 44, 44–45 aspartate aminotransferase  58, 59 glutamate decarboxylase  130 complexes with non-protein AAs  525 in cysteine synthase complex  222 pyridoxal kinase (PK)  58, 60 pyruvate decarboxylase (PDC)  267 pyruvate dehydrogenase complex  280, 282 pyruvate family stress response pathway  264, 267–270 pyruvate kinases (PK) activity engineering with knockout mutants  291 influence of Asp and Glu  288, 289–290, 290 function in plastids  280 structures and properties  288, 289 quality protein maize  243 quantitative real-time PCR analysis  202, 209 racemization  169, 491–492, 552–553 radioimmunoassays  396, 409 radiolabelling  299–300, 322 reactive oxygen species (ROS) accumulation in stress conditions  204, 226 detoxification by free AAs  263 H2O2 and polyamine-mediated signalling  145, 183–184 photocatalysed production  467 scavenging ability of GABA  135, 137 of melatonin  395, 407–409, 412 synergism with NO  556 repeat dose toxicity  471–472 research currect focus and recent advances  539–541, 566–569, 567 epidemiological, and public health ­concerns  472–473 future objectives and needs  329–330, 572–573 innovative directions and technologies  509, 570–572 residues, agrochemical  465–466, 475 respiration, supplying energy for N assimilation  278–279, 280–282 rhizobitoxine 450, 450 rhizosphere amino acid exchange processes  301–302, 306, 330 root–soil microbe interactions  318, 320–321, 443 roots development, effect of NOS activity  147–148, 164 exudates (amino acid secretion)  306, 317, 454 hemiparasitic associations  324–325 mycorrhizal associations  321–323 nitrogen uptake by root hairs  317 nodules and rhizobia  306–307, 323–324, 515 role of glutamine synthetase  84, 85, 92–93 uptake of glyphosate  464, 468 Roundup® 461–462 see also glyphosate saccharopine dehydrogenase (SDH)  240–243, 272 salicylic acid (SA) biosynthesis  526, 547, 548, 569 signalling, in stress and defence  547–549, 554, 563, 568 synergistic and antagonistic interactions  556 salt tolerance  186, 265, 543 SAM (/SAMDC) see S-adenosylmethionine (/decarboxylase) sample preparation (for AA analysis)  482 SAT see serine acetyltransferase secondary compounds  363, 363, 508–509, 540, 549–550 seeds export of amino acids from coat  300 germination  105–106, 164, 329 maturation 108–109 non-protein amino acid content  508 protein content  117–118 selenoamino acids human therapeutic potential  529 metabolism and toxicity  515, 519, 521, 523 structures and occurrence  510, 512 selenomethionine  513, 519 senescence  108, 149, 185–186, 228–229, 379–380 Index 595 serine (Ser) phosphorylation 491 recovery in acid hydrolysis  483, 486 serine acetyltransferase (SERAT, SAT) genetic regulation gene expression patterns  202–204, 203 SERAT gene family structures  196, 197, 198–199 transgenic overexpression  206–207 metabolic functions  195–196, 211–212 analysis using knockout mutants  204, 204–206, 205 phylogeny 222, 223 properties and localization  197, 199, 199, 200 as part of cysteine synthase complex  199–202, 200, 222–224, 223 serine hydroxylmethyltransferase (SHM) genes  210–211 serine:glyoxylate aminotransferase (SGAT)  47 serotonin (5-hydroxytryptamine) occurrence in plants, and effects on ­animals  375–377 role in defence against grass crop ­pathogens  377–379, 380 role in senescence  379–380 serotonin N-acetyltransferase (SNAT)  391, 400, 402–403, 406 shade avoidance (SAV 3)  343, 351 shikimate pathway in aromatic compound biosynthesis  71 blockage by glyphosate  462, 569 signal transduction  553–554, 555 abscisic acid  556, 558 direct and indirect roles of AAs  299, 540, 551–552, 553–554, 555 ethylene  545, 556 hydrogen peroxide  183–184 integration of signal cascades  558–559, 563, 567, 570–571 jasmonate  556, 558, 565 nitric oxide  142 roles of non-protein amino acids  510, 526–527 salicylic acid  547–549 slope-ratio assays  500, 500–501, 502 SMCO (S-methylcysteine sulfoxide)  513, 519, 523–524, 527, 528 spermidine (Spd)  166, 526 biosynthesis  179, 180 spermidine synthase (SPDS)  181, 185 spermine (Spm)  166 biosynthesis  179, 180, 181–182 spermine synthase (SPMS)  181–182 stress biology  48–50 stress metabolism general model  563–564, 564, 572 response metabolic pathways  540, 567 asparagine synthesis in C depletion  107–108, 271 GABA shunt  135–136, 136, 267 mitigation by non-protein AAs  509, 525–527 oxygen deficiency responses  267–270, 269 polyamines, protective roles  186 proline accumulation  264–267 specific responses  525, 561–562 biotic stresses  442, 559–560, 563, 564–565 environmental stresses  562–563 environmental (abiotic) stresses  262–263, 560, 562–563 see also defence responses succinic semialdehyde dehydrogenase (SSADH)  135, 136, 267 sulfate reduction  206, 221 uptake and transport  208, 220–221 S-sulfocysteine synthase (CS26)  225–226 sulfur amino acids analogues  510, 513, 519, 545 availability in foods  501 metabolic roles in plants  544–545 sulfur metabolism  105, 195–196, 196, 219–220 surfactants, toxicity  471 synergistic interactions  556, 557 synthetases/synthases inhibitors 450–453 specific types asparagine synthetase  102–116 glutamine synthetase  83–93 nitric oxide synthase  145–150 systemic acquired resistance (SAR)  228, 547, 559 systemin  540, 559 tabtoxin 451, 452 TCA (tricarboxylic acid) cycle activity in seeds  109 bypassed by GABA shunt  135 contribution of (nutritionally) essential AAs 272 effect of exogenous l- and d-Orn 169–170 modulation in hypoxia  46, 50 regulation and flux control  280, 283 teratogenicity, risk assessment  473–474 tetrahydrobiopterin (BH4) 145 thermospermine (T-Spm)  179, 180, 182 threonine (Thr)  234, 235, 236, 237 endogenous dietary losses  498 in foods, effects of processing  491 metabolic availability assessment  501, 502 recovery in acid hydrolysis  483, 486 threonine dehydratase (TD)  565, 571 Tobacco mosaic virus (TMV)  149 TOR regulation  91, 184–185 596 Index toxicology biochemical toxicity mechanisms  522–525 classification of adverse effects  514 dose dependence  474–475 testing and standards  469–472 types of toxicity carcinogens and cancer risks  472–473 developmental/reproductive toxicity  473–474 endocrine disruption testing  474 genotoxicity 472 goitrogenic toxins  443, 520 neurotoxins  474, 519 see also phytotoxins transaminases see aminotransferases transcription factors  89, 441, 570 transcriptional gene regulation  88–89, 257 translational regulation  91 transpiration stream  325–326 transport inhibitor response  343, 352 transporter proteins families, in amino acid transport  137, 302–305, 304, 320 glucosinolate symporters (GTR) 440 regulation  305–306, 307, 318 sulfate transporters  220–221 tryptamine (TAM) pathway  347–348 tryptophan (Trp) biosynthetic pathway branch points  365, 366, 438 reactions and enzymes  362–363 regulation 363–364 secondary products  363, 363, 549, 563 as precursor of melatonin  390, 396 quantitative determination  483–485, 484, 485, 486 tryptophan 5-hydroxylase (T5H)  396, 399, 401, 404–405 tryptophan decarboxylase (TDC)  347, 378, 399, 401–402, 405–406 tyrosine (Tyr) biosynthesis in bacteria  71–73, 72 in plants  73, 73, 548, 549 phosphorylation and nitration  92, 554, 567 recovery in acid hydrolysis  483 residue Y225 in AspAT apoprotein  60, 62 in stress/defence responses  563 m-tyrosine phytotoxicity  454, 455 tyrosine aminotransferase anabolic roles  71–73 aromatic amino acid biosynthesis  71–73, 72, 77 synthesis of secondary metabolites  77–78 enzyme characterization purification 74, 74 reaction kinetics  74–76, 75, 76 reactions catalysed  74, 75 structure 79 substrate specificity  76, 76 in vivo activity assays  76–77, 77 UDP-glycosyltransferases (UGT)  369 urea cycle analogues and congeners  510, 518, 524–525 in animals  169 in nitrogen metabolism, pathways  143, 144, 522 arginine/canavanine synthesis  512–513, 513, 542 urease 144 3'-UTR-mediated transcript destabilization  90 vacuolar membrane transport  302 valine (Val)  270, 546 victorin  543, 550 viniferins 375 vitamin B6 photolysis by UV-B, homeostatic response  63 vitamers and roles in plants  58 weed control see herbicides wheat (Triticum aestivum) 367–367 World Health Organization (WHO) chemical safety assessments  469, 475, 476 dietary guidelines  234 wound response  167, 559–560, 564–565 xylem amino acid import/export  299–301, 305, 326, 328–329 N transport compounds in tree sap  326–328, 327 Yang cycle  344, 544, 545 yield (crops) see crop yield zeolin 245