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Identification of Subcellular, Structural, and Metabolic Changes Through NMR

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Phenomics in Crop Plants: Trends, Options and Limitations

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Abstract

Secondary metabolites are unique sources for flavors, nutraceuticals, pharmaceuticals, and industrial bioactive molecules which are biosynthesized in different plant tissues. These metabolites play a major role in the adaptation of plants to the prevailing environment, in overcoming stress conditions, and in defense to several unforeseen invasions. Identifying the biological components and their functions and multiple interactions between components to understand the cellular metabolism of a cell to meet its fluctuating demand for energy and materials has remained a challenging task. Based on traditional metabolic analysis, mapping of intracellular fluxes in metabolic networks is only possible with high-throughput techniques. Nuclear magnetic resonance (NMR) spectroscopy is a powerful and versatile tool that can provide information on the metabolites and their metabolic network. NMR has played a dominant role in the identification of an array of compounds from diverse environments and diverse ecogeographic domains. Plant biotic relationships which include host plant interaction and resistance for an eco-metabolomics have been developed with NMR approach. NMR can also be used to determine low-resolution structures of target–ligand complexes for natively unstructured proteins or membrane proteins that are not amenable to crystallographic approaches.

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References

  • Abdel-Farid IB, Jahangir M, van den Hondel CAMJJ, Kim HK, Choi YH, Verpoorte R (2009) Fungal infection-induced metabolites in Brassica rapa. Plant Sci 176:608–615

    Article  CAS  Google Scholar 

  • Ali K, Maltese F, Zyprian E, Rex M, Choi HY, Verpoorte R (2009) NMR metabolomic fingerprinting based identification of grapevine metabolites associated with downy mildew resistance. J Agric Food Chem 57:9599–9606

    Article  CAS  PubMed  Google Scholar 

  • Allwood JW, Ellis DI, Goodacre R (2008) Metabolomic technologies and their application to the study of plants and plant-host interactions. Physiol Plant 132:117–135

    CAS  PubMed  Google Scholar 

  • Aubert S, Hennion F, Bouchereau A, Gout E, Bligny R, Dorne AJ (1999) Subcellular compartmentation of proline in the leaves of the subantarctic Kerguelen cabbage Pringlea antiscorbutica R. Br. In vivo 13C-NMR study. Plant Cell Environ 22:255–259

    Article  CAS  Google Scholar 

  • Avelange-Macherel M-H, Ly-Vu B, Delauny J, Richomme P, Leprince O (2006) NMR metabolite profiling analysis reveals changes in phospholipid metabolism associated with the re-establishment of desiccation tolerance upon osmotic stress in germinated radicals of cucumber. Plant Cell Environ 29:471–482

    Article  CAS  PubMed  Google Scholar 

  • Bailey NJC, Oven M, Holmes E, Nicholson JK, Zenk MH (2003) Metabolomic analysis of the consequences of cadmium exposure in Silene cucubalus cell cultures via 1H NMR spectroscopy and chemometrics. Phytochemistry 62:851–858

    Article  CAS  PubMed  Google Scholar 

  • Bligny R, Douce R (2001) NMR and plant metabolism. Curr Opin Plant Biol 4:191–196

    Article  CAS  PubMed  Google Scholar 

  • Boothe JG, Sönnichsen FD, de Beus MD, Johnson-Flanagan AM (1997) Purification, characterization, and structural analysis of a plant low-temperature-induced protein. Plant Physiol 113(2):367–376

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Cabrera HM, Munoz O, Zuniga GE, Corcuera LJ, Argandona VH (1995) Changes in ferulic acid and lipid content in aphid-infested barley. Phytochemistry 39:1023–1026

    Article  CAS  Google Scholar 

  • Charlton AJ, Donarksi JA, Harrison M, Jones SA, Godward J, Oehlschlager S, Arques JL, Ambrose M, Chinoy C, Mullineaux PM, Domoney C (2008) Responses of the pea (Pisum sativum L.) leaf metabolome to drought stress assessed by nuclear magnetic resonance spectroscopy. Metabolomics 4:312–327

    Article  CAS  Google Scholar 

  • Chaves MM, Maroco JP, Pereira JS (2003) Understanding plant responses to drought – from genes to the whole plant. Funct Plant Biol 30:239–264

    Article  CAS  Google Scholar 

  • Choi HK, Choi YH, Verberne M, Lefeber AWM, Erkelens C, Verpoorte R (2004a) Metabolic fingerprinting of wild type and transgenic tobacco plants by 1 H-NMR and multivariate analysis techniques. Phytochemistry 65:857–864

    Article  CAS  PubMed  Google Scholar 

  • Choi YH, Kim HK, Hazekamp A, Erkelens C, Lefeber AMW, Verpoorte R (2004b) Metabolomic differentiation of Cannabis sativa cultivars using 1H-NMR and principal component analysis. J Nat Prod 67:953–957

    Article  CAS  PubMed  Google Scholar 

  • Choi YH, Tapias EC, Kim HK, Lefeber AWM, Erkelens C, Verhoeven JTJ, Brzin J, Zei J, Verpoorte R (2004c) Metabolic discrimination of Catharantus roseus leaves infected by phytoplasma using 1H-NMR spectroscopy and multivariate data analysis. Plant Physiol 135:2398–2410

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Choi YH, Sertic S, Wilson EG, Michopoulos F, Lefeber AWM, Erkelens C, Kricun SPD, Verpoorte R (2005) Classification of Ilex species based on metabolomic fingerprinting using nuclear magnetic resonance and multivariate data analysis. J Agric Food Chem 53:1237–1245

    Article  CAS  PubMed  Google Scholar 

  • Choi YH, Kim HK, Linthorst HJM, Hollander JG, Lefeber AWM, Erkenlens C, Nuzillard J-M, Verpoorte R (2006) NMR metabolomics to revisit the tobacco mosaic virus infection in Nicotiana tabacum leaves. J Nat Prod 69:742–748

    Article  CAS  PubMed  Google Scholar 

  • Davis KR, Darvill AG, Albersheim P (1986) Several biotic and abiotic elicitors and synergistically in the induction of phytoalexin accumulation in soybean. Plant Mol Biol 6:23–32

    Article  CAS  PubMed  Google Scholar 

  • De Costa F, Yendo ACA, Fleck JD, Gosmann G, Fett-Netto (2013) Accumulation of a bioactive triterpene saponin fraction of Quillaja brasiliensis leaves is associated with abiotic and biotic stresses. Plant Physiol Biochem 66:56–62

    Article  PubMed  Google Scholar 

  • Delgado NJ, Casler MD, Grau CR, Jung HG (2002) Reactions of smooth bromegrass clones with divergent lignin or etherified ferulic acid concentration to three fungal pathogens. Crop Sci 42:1824–1831

    Article  Google Scholar 

  • El-Sayed AA, Razin AM, Swaety HMF, Mohamed SM, Abou-Aitah KEA (2008) Effect of water stress on yield and bioactive chemical constituents of Tribulus species. J Appl Sci Res 4:2134–2144

    Google Scholar 

  • Fan TW-M, Lane AN (2008) Structure-based profiling of metabolites and isotopomers by NMR. Progr Nucl Magn Reson Spectr 52:69–117

    Article  CAS  Google Scholar 

  • Fernie AR, Willmitzer L (2004) Carbohydrate metabolism. In: Christou P, Klee HK (eds) The handbook of plant biotechnology. Wiley, Hoboken

    Google Scholar 

  • Figueiredo A, Fortes AM, Ferreira S, Sebastiana M, Choi YH, Sousa L, Acioli-Santos B, Pessoa F, Verpoorte R, Pais MS (2008) Transcriptional and metabolic profiling of grape (Vitis vinifera L.) leaves unravel possible innate resistance against pathogenic fungi. J Exp Bot 59:3371–3381

    Article  CAS  PubMed  Google Scholar 

  • Frasier PD, Enfissi EMA, Goodfellow M, Eguchi T, Bramley PM (2007) Metabolite profiling of plant carotenoids using the matrix assisted laser desorption ionization time-of-flight mass spectrometry. Plant J 49:552–564

    Article  Google Scholar 

  • Gomez-Vasques R, Day R, Buschmann H, Randles S, Beeching JR, Cooper RM (2004) Phenylpropanoids, phenylalanine ammonia lyase and peroxidases in elicitor-challenged cassava (Manihot esculenta) suspension cells and leaves. Ann Bot 94:87–97

    Article  Google Scholar 

  • Harkes P, Krijbolder L, Libbenga K, Wijnsma R, Nsengiyaremge T, Verpoorte R (1985) Influence of various media constituents on the growth of Cinchona ledgeriana tissue cultures and the production of alkaloids and anthraquinones. Plant Cell Tissue Organ Cult 4:199–214

    Article  CAS  Google Scholar 

  • Hemminga MA, Visser J (2000) NMR in biotechnology. J Biotechnol 77:1–3

    Article  CAS  PubMed  Google Scholar 

  • Hernandez JA, Jimenez A, Mullineaux P, Sevilla F (2000) Tolerance of pea (Pisum sativum L.) to long-term salt stress is associated with induction of antioxidant defences. Plant Cell Environ 23:853–862

    Article  CAS  Google Scholar 

  • Horbowicz M, Kosson R, Wiczkowski W, Koczkodaj D, Mitrus J (2010) The effect of methyl jasmonate on accumulation of 2-phenylethylamine and putrescine in seedlings of common buckwheat (Fagopyrum esculentum). Acta Physiol Plant 33:897–903

    Article  Google Scholar 

  • Ishikawa M, Price WS, Ide H, Arata Y (1997) Visualization of freezing behaviors in leaf and flower buds of full-moon maple by nuclear magnetic resonance microscopy. Plant Physiol 115:1515–1524

    PubMed Central  CAS  PubMed  Google Scholar 

  • Jahangir M, Abdel-Farid IB, Choi YH, Verpoorte R (2008a) Metal ion-inducing metabolite accumulation in Brassica rapa. J Plant Physiol 165:1429–1437

    Article  CAS  PubMed  Google Scholar 

  • Jahangir M, Kim HK, Choi YH, Verpoorte R (2008b) Metabolomic response of Brassica rapa submitted to pre-harvest bacterial contamination. Food Chem 107:362–368

    Article  CAS  Google Scholar 

  • Karuppusamy S (2009) A review on trends in production of secondary metabolites from higher plants by in vitro tissue, organ and cell cultures. J Med Plants Res 3:1222–1239

    CAS  Google Scholar 

  • Keen NT, Partiridge JE, Zaki AI (1972) Pathogen-produced elicitor of a chemical defence mechanism in soybean mono-genically resistant to Phytophora megasperma var. sojae. Phytopathology 62:768

    Google Scholar 

  • Keifer PA (1999) NMR tools for biotechnology. Curr Opin Biotechnol 10:34–41

    Article  CAS  PubMed  Google Scholar 

  • Kirk H, Choi YH, Kim HK, Verpoorte R, van der Meijden E (2005) Comparing metabolomes: the chemical consequences of hybridization in plants. New Phytol 167:613–622

    Article  CAS  PubMed  Google Scholar 

  • Kliebenstein DJ et al (2001) Genetic control of natural variation in Arabidopsis glucosinolate accumulation. Plant Physiol 126(2):811–825

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kliebenstein D et al (2002) Comparative analysis of quantitative trait loci controlling glucosinolates, myrosinase and insect resistance in Arabidopsis thaliana. Genetics

    Google Scholar 

  • Köckenberger W (2001a) Functional imaging of plants by magnetic resonance experiments. Trends Plant Sci 6:286–292

    Article  PubMed  Google Scholar 

  • Köckenberger W (2001b) Nuclear magnetic resonance micro-imaging in the investigation of plant cell metabolism. J Exp Bot 52:641–652

    Article  PubMed  Google Scholar 

  • Le Gall G, Dupont MS, Mellon FA, Davis AL, Collins GJ, Verhoeyen ME, Colquhoun IJ (2003) Characterization and content of flavonoid glycosides in genetically modified tomato (Lycopersicon esculentum) fruits. J Agric Food Chem 51:2438–2446

    Article  PubMed  Google Scholar 

  • Le Lay P, Isaure MP, Sarry JE, Kuhn L, Fayard B, Le Bail JL, Bastien O, Garin J, Roby C, Bourguignon J (2006) Metabolomic, proteomic and biophysical analyses of Arabidopsis thaliana cells exposed to caesium stress. Influence of potassium supply. Biochemie 88:153–1547

    Google Scholar 

  • Leiss KA, Choi YH, Abdel-Farid IB, Verpoorte R, Klinkhamer PGL (2009a) NMR metabolomics of thrips (Frankliniella occidentalis) resistance in Senecio hybrids. J Chem Ecol 35:219–229

    Article  CAS  PubMed  Google Scholar 

  • Leiss KA, Maltese F, Choi YH, Verpoorte R, Klinkhamer PGL (2009b) Identification of chlorogenic acid as a resistance factor for thrips in Chrysanthemum. Plant Physiol 150:1567–1575

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Leiss KA, Choi YH, Verpoorte R, Klinkhamer PGL (2011) An overview of NMR-based metabolomics to identify secondary plant compounds involved in host plant resistance. Phytochem Rev 10:205–216

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Lens P, Hemminga MA (2001) Special issue on NMR in environmental biotechnology—introduction. J Ind Microbiol Biotechnol 26:1

    Article  CAS  PubMed  Google Scholar 

  • Liang YS, Choi YH, Kim HK, Linthorst HJ, Verpoorte R (2006) Metabolomic analysis of methyl jasmonate treated Brassica rapa leaves by 2-dimensional NMR spectroscopy. Phytochemistry 67:2503–2511

    Article  CAS  PubMed  Google Scholar 

  • Lin JT, Chen SL, Liu SC, Yang DJ (2009) Effect of harvest time on saponins in yam (Dioscorea pseudojaponica Yamamoto). J Food Drug Anal 17:116–122

    CAS  Google Scholar 

  • Liu YS, Gur A, Ronen G, Causse M, Damidaux R, Buret M, Hirschberg J, Zamir D (2003) There is more to tomato fruit colour than candidate carotenoid genes. Plant Biotechnol J 1:195–207

    Article  CAS  PubMed  Google Scholar 

  • Mirnezhad M, Romero-Gonza’lez RR, Leiss KA, Choi YH, Verpoorte R, Klinkhamer PGL (2010) Metabolomic analysis of host plant resistance to thrips in wild and cultivated tomatoes. Phytochem Anal 21:110–117

    Article  CAS  PubMed  Google Scholar 

  • Moose SP, Dudley JW, Rocheford TR (2004) Maize selection passes the century mark: a unique resource for 21st century genomics. Trends Plant Sci 9:358–364

    Article  CAS  PubMed  Google Scholar 

  • Murch SJ, Haq K, Rupasinghe HPV, Saxena PK (2003) Nickel contamination affects growth and secondary metabolite composition of St. John’s wort (Hypericum perforatum L.). Environ Exp Bot 49:251–257

    Article  CAS  Google Scholar 

  • Nussbaumer P, Kapetanidis T, Christen P (1998) Hairy roots of Datura candida × D. aurea: effect of culture medium composition on growth and alkaloid biosynthesis. Plant Cell Rep 17:405–409

    Article  CAS  Google Scholar 

  • Odjegba Victor J, Alokolaro AA (2013) Simulated drought and salinity modulates the production of phytochemicals in Acalypha wilkesiana. J Plant Stud 2:2

    Google Scholar 

  • Perez AG, Sanz C, Olias R, Olias JM (1997) Effect of methyl jasmonate on in vitro strawberry ripening. J Agric Food Chem 45:3733–3737

    Article  CAS  Google Scholar 

  • Perez-Balibrea S, Moreno DA, Garcia-Viguera C (2008) Influence of light on health- promoting phytochemicals of broccoli sprouts. J Sci Food Agric 88:904–910

    Article  CAS  Google Scholar 

  • Pfeffer PE, Bago B, Shachar-Hill Y (2001) Exploring mycorrhizal function with NMR spectroscopy. New Phytol 150:543–553

    Article  CAS  Google Scholar 

  • Ratcliffe RG, Shachar-Hill Y (2001) Probing plant metabolism with NMR. Annu Rev Plant Physiol Plant Mol Biol 52:499–526

    Article  CAS  PubMed  Google Scholar 

  • Ratcliffe RG, Roscher A, Shachar-Hill Y (2001) Plant NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 39:267–300

    Article  Google Scholar 

  • Roberts JKM (2000) NMR adventures in the metabolic labyrinth within plants. Trends Plant Sci 5:30–34

    Article  CAS  PubMed  Google Scholar 

  • Salywon AM, Dierig DA, Rebman JP, de Rodri’guez DJ (2005) Evaluation of new Lesquerella and Physaria (Brassicaceae) oilseed germplasm. Am J Bot 92:53–62

    Article  PubMed  Google Scholar 

  • Schauer N, Fernie AR (2006) Plant metabolomics: towards biological function and mechanism. Trends Plant Sci 11:508–516

    Article  CAS  PubMed  Google Scholar 

  • Sharma P, Jha AB, Dubey RS, Pessarakli M (2012) Reactive oxygen species, oxidative damage, and antioxidant defense mechanism in plants under stressful conditions. J Bot 2:1–26

    Article  CAS  Google Scholar 

  • Silvente S, Sobolev AP, Lara M (2012) Metabolite adjustments in drought tolerant and sensitive soybean genotypes in response to water stress. PLoS One 7(6):e38554

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Snaar JEM, van As H (1992) Probing water compartment and membrane permeability in plant cells by proton NMR relaxation measurements. Biophys J 63:1654–1658

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Sudha G, Ravishankar GA (2003a) Influence of methyl jasmonate and salicylic acid in the enhancement of capsaicin production in cell suspension cultures of Capsicum frutescens mill. Curr Sci 85:1212–1217

    CAS  Google Scholar 

  • Sudha G, Ravishankar GA (2003b) Elicitation of anthocyanin production in callus cultures of Daucus carota and involvement of calcium channel modulators. Curr Sci 84:775–779

    CAS  Google Scholar 

  • Tieman D et al (2006) Tomato aromatic amino acid decarboxylases participate in synthesis of the flavor volatiles 2-phenylethanol and 2-phenylacetaldehyde. Proc Natl Acad Sci U S A 103(21):8287–8292

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • van der Fits L, Memelink J (2000) ORCA3, a jasmonate responsive transcriptional regulator of plant primary and secondary metabolism. Science 289:295–297

    Article  PubMed  Google Scholar 

  • van der Weerd I, Claessens MMAE, Efdé C, van As H (2002) Nuclear magnetic resonance imaging of membrane permeability changes in plants during osmotic stress. Plant Cell Environ 25:1539–1549

    Article  Google Scholar 

  • Verpoorte R, Choi YH, Kim HK (2007) NMR-based metabolomics at work in phytochemistry. Phytochem Rev 6:3–14

    Article  CAS  Google Scholar 

  • Verpoorte R, Choi YH, Mustafa NR, Kim HK (2008) Metabolomics: back to basics. Phytochem Rev 7:525–537

    Article  CAS  Google Scholar 

  • Wang ML, Morris JB, Tonnis B, Pinnow D, Davis J, Raymer P, Pederson GA (2011) Screening of the entire USDA castor germplasm collection for oil content and fatty acid composition for optimum biodiesel production. J Agric Food Chem 59:9250–9256

    Article  CAS  PubMed  Google Scholar 

  • Ward JL, Baker JM, Beale MH (2001) Recent applications of NMR spectroscopy in plant metabolomics. FEBS J 274:1126–1131

    Article  Google Scholar 

  • Watanabe T, Osaki M, Yano H, Rao IM (2006) Internal mechanisms of plant adaptation to aluminum toxicity and phosphorus starvation in three tropical forages. J Plant Nutr 29:1243–1255

    Article  CAS  Google Scholar 

  • Wenzl P, Chaves AL, Mayer JE, Rao IM, Nair MG (2000) Roots of nutrient-deprivedBrachiaria species accumulate 1,3-di-0- trans-feruloylquinic acid. Phytochemistry 55:389–395

    Article  CAS  PubMed  Google Scholar 

  • Wenzl P, Chaves AL, Patiño GM, Mayer JE, Rao IM (2002) Aluminum stress stimulates the accumulation of aluminum detoxifying organic acids in root apices of Brachiaria species. J Plant Nutr Soil Sci 165:582–588

    Article  CAS  Google Scholar 

  • Ye Y, Zhang L, Yang R, Luo Q, Chen H, Yan X, Tang H (2013) Metabolic phenotypes associated with high-temperature tolerance of Porphyra haitanensis strains. J Agric Food Chem 61:8356–8363

    Article  CAS  PubMed  Google Scholar 

  • Zhang WH, Jones GP (1996) Water permeability in wheat root protoplasts determined from nuclear magnetic resonance relaxation times. Plant Sci 118:97–106

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Plant Biotechnology, Indian Institute of Integrative Medicine Research, Kanal Road, Jammu, Jammu and Kashmir, India

    Rekha Sapru Dhar

  2. Division of Crop Improvement, ICAR – Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, Uttar Pradesh, India

    Nupur Malviya

Authors
  1. Rekha Sapru Dhar
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  2. Nupur Malviya
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Correspondence to Rekha Sapru Dhar .

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Editors and Affiliations

  1. Division of Crop Improvement, ICAR - Indian Institute of Pulses Research, Kalyanpur, Kanpur, Uttar Pradesh, India

    Jitendra Kumar

  2. Division of Crop Improvement, ICAR - Indian Institute of Pulses Research, Kalyanpur, Kanpur, Uttar Pradesh, India

    Aditya Pratap

  3. Rabat - Instituts, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco

    Shiv Kumar

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Dhar, R.S., Malviya, N. (2015). Identification of Subcellular, Structural, and Metabolic Changes Through NMR. In: Kumar, J., Pratap, A., Kumar, S. (eds) Phenomics in Crop Plants: Trends, Options and Limitations. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2226-2_13

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