Quantitative metabolic profiles of tomato flesh and seeds during fruit development: complementary analysis with ANN and PCA

Tomato, an essential crop in terms of economic importance and nutritional quality, is also used as a model species for all fleshy fruits and for genomics of Solanaceae. Tomato fruit quality at harvest is a direct function of its metabolite content, which in turn is a result of many physiological changes during fruit development. The aim of the work reported here was to develop a global approach to characterize changes in metabolic profiles in two interdependent tissues from the same tomato fruits. Absolute quantification data of compounds in flesh and seeds from 8 days to 45 days post anthesis (DPA) were obtained through untargeted (proton nuclear magnetic resonance, 1H-NMR) and targeted metabolic profiling (liquid chromatography with diode array detection (LC-DAD) or gas chromatography with flame ionization detection (GC-FID)). These data were analyzed with chemometric approaches. Kohonen self organizing maps (SOM) analysis of these data allowed us to combine multivariate (distribution of samples on Kohonen SOMs) and univariate information (component plane representation of metabolites) in a single analysis. This strategy confirmed published data and brought new insights on tomato flesh and seed composition, thus demonstrating its potential in metabolomics. The compositional changes were related to physiological processes occurring in each tissue. They pointed to (i) some parallel changes at early stages in relation to cell division and transitory storage of carbon, (ii) metabolites participating in the fleshy trait and (iii) metabolites involved in the specific developmental patterns of the seeds.

[1]  G. Savage,et al.  Antioxidant activity in different fractions of tomatoes , 2005 .

[2]  C. Parsons,et al.  Nutritional evaluation of dried tomato seeds. , 2003, Poultry science.

[3]  M. Causse,et al.  Cell Expansion and Endoreduplication Show a Large Genetic Variability in Pericarp and Contribute Strongly to Tomato Fruit Growth1 , 2005, Plant Physiology.

[4]  P. Fraser,et al.  Application of high-performance liquid chromatography with photodiode array detection to the metabolic profiling of plant isoprenoids: Metabolic profiling of isoprenoids , 2008 .

[5]  J. Labavitch,et al.  Cell Wall Metabolism in Ripening Fruit: I. CELL WALL CHANGES IN RIPENING ;BARTLETT' PEARS. , 1980, Plant physiology.

[6]  Fernando Carrari,et al.  Metabolic Profiling of Transgenic Tomato Plants Overexpressing Hexokinase Reveals That the Influence of Hexose Phosphorylation Diminishes during Fruit Development , 2003, Plant Physiology.

[7]  A. Fernie,et al.  Journal of Experimental Botany, Page 1 of 11 Metabolomics and Metabolic Profiling Special Issue , 2004 .

[8]  M. Petreikov,et al.  Sucrose-to-Starch Metabolism in Tomato Fruit Undergoing Transient Starch Accumulation , 1997, Plant physiology.

[9]  P. White.  Recent advances in fruit development and ripening: an overview. , 2002, Journal of experimental botany.

[10]  Alison M. Smith,et al.  Starch metabolism in developing embryos of oilseed rape , 1997, Planta.

[11]  J. Bewley,et al.  A Role for the Surrounding Fruit Tissues in Preventing the Germination of Tomato (Lycopersicon esculentum) Seeds : A Consideration of the Osmotic Environment and Abscisic Acid. , 1992, Plant physiology.

[12]  B. Denoyes-Rothan,et al.  Quantitative metabolic profiling by 1-dimensional 1H-NMR analyses: application to plant genetics and functional genomics. , 2004, Functional plant biology : FPB.

[13]  Lloyd W Sumner,et al.  Biomarker metabolites capturing the metabolite variance present in a rice plant developmental period , 2005, BMC Plant Biology.

[14]  D. M. Pharr,et al.  Carbohydrate Changes during Maturation of Cucumber Fruit : Implications for Sugar Metabolism and Transport. , 1983, Plant physiology.

[15]  J. Deverna,et al.  Sink Metabolism in Tomato Fruit : IV. Genetic and Biochemical Analysis of Sucrose Accumulation. , 1991, Plant physiology.

[16]  David A. Jones,et al.  myo-Inositol and sucrose concentrations affect the accumulation of raffinose family oligosaccharides in seeds. , 2004, Journal of experimental botany.

[17]  A. Kinney,et al.  VARIATIONS IN THE BIOSYNTHESIS OF SEED-STORAGE LIPIDS. , 2001, Annual review of plant physiology and plant molecular biology.

[18]  J. Palatnik,et al.  Changes in amino acid composition and nitrogen metabolizing enzymes in ripening fruits of Lycopersicon esculentum Mill. , 2000, Plant science : an international journal of experimental plant biology.

[19]  David Latshaw,et al.  Analyses of tomato peel and seed byproducts and their use as a source of carotenoids , 2005 .

[20]  John C. Lindon,et al.  Pattern recognition methods and applications in biomedical magnetic resonance , 2001 .

[21]  D Côme,et al.  Changes in oligosaccharide content and antioxidant enzyme activities in developing bean seeds as related to acquisition of drying tolerance and seed quality. , 2001, Journal of experimental botany.

[22]  F. Vos,et al.  A rapid and inexpensive microplate assay for the enzymatic determination of glucose, fructose, sucrose, L-malate and citrate in tomato (Lycopersicon esculentum) extracts and in orange juice. , 2001, Phytochemical analysis : PCA.

[23]  Sovan Lek,et al.  A comparison of self-organizing map algorithm and some conventional statistical methods for ecological community ordination , 2001 .

[24]  J. Labavitch,et al.  Cell Wall Metabolism in Ripening Fruit : V. Analysis of Cell Wall Synthesis in Ripening Tomato Pericarp Tissue Using a d-[U-C]Glucose Tracer and Gas Chromatography-Mass Spectrometry. , 1991, Plant physiology.

[25]  P. Fraser,et al.  Identification and quantification of carotenoids, tocopherols and chlorophylls in commonly consumed fruits and vegetables. , 2003, Phytochemistry.

[26]  M. Cámara,et al.  FATTY ACID COMPOSITION OF TOMATO POMACE , 2001 .

[27]  Robert L. Shewfelt,et al.  Absence of a clear relationship between lipid pathway enzymes and volatile compounds in fresh tomatoes , 2001 .

[28]  J. Giovannoni.  Genetic Regulation of Fruit Development and Ripening , 2004, The Plant Cell Online.

[29]  A. Bennett,et al.  Sink Metabolism in Tomato Fruit : III. Analysis of Carbohydrate Assimilation in a Wild Species. , 1988, Plant physiology.

[30]  G. Seifert,et al.  Nucleotide sugar interconversions and cell wall biosynthesis: how to bring the inside to the outside. , 2004, Current opinion in plant biology.

[31]  Teuvo Kohonen,et al.  Self-Organizing Maps , 2010 .

[32]  M. Biran,et al.  NMR study of low subcellular pH during the development of cherry tomato fruit , 2000 .

[33]  Jens Nielsen,et al.  The next wave in metabolome analysis. , 2005, Trends in biotechnology.

[34]  H. Heldt,et al.  Free Amino Acid Composition of Phloem Sap and Growing Fruit of Lycopersicon esculentum , 1998 .

[35]  L. Kunst,et al.  All fatty acids are not equal: discrimination in plant membrane lipids. , 2000, Trends in plant science.

[36]  L. Barantin,et al.  Concentration Measurement by Proton NMR Using the ERETIC Method. , 1999, Analytical chemistry.

[37]  C. Kent,et al.  Eukaryotic phospholipid biosynthesis. , 1995, Annual review of biochemistry.

[38]  R. Bino,et al.  The tomato seed as a model system to study seed development and germination. , 1998 .

[39]  R. Bino,et al.  The light-hyperresponsive high pigment-2dg mutation of tomato: alterations in the fruit metabolome. , 2005, The New phytologist.

[40]  K. Bradford,et al.  Expression of a GALACTINOL SYNTHASE Gene in Tomato Seeds Is Up-Regulated before Maturation Desiccation and Again after Imbibition whenever Radicle Protrusion Is Prevented1 , 2003, Plant Physiology.

[41]  J. Ozga,et al.  Hormonal Interactions in Fruit Development , 2003, Journal of Plant Growth Regulation.

[42]  J F Morot-Gaudry.  Functional Plant Genomics , 2007 .

[43]  B. Whitaker.  Changes in the steryl lipid content and composition of tomato fruit during ripening , 1988 .

[44]  G. Le Gall,et al.  Metabolite profiling of tomato (Lycopersicon esculentum) using 1H NMR spectroscopy as a tool to detect potential unintended effects following a genetic modification. , 2003, Journal of agricultural and food chemistry.

[45]  A. Segre,et al.  Nuclear Magnetic Resonance Spectroscopy-Based Metabolite Profiling of Transgenic Tomato Fruit Engineered to Accumulate Spermidine and Spermine Reveals Enhanced Anabolic and Nitrogen-Carbon Interactions1[W][OA] , 2006, Plant Physiology.

[46]  M. Zanor,et al.  Integrated Analysis of Metabolite and Transcript Levels Reveals the Metabolic Shifts That Underlie Tomato Fruit Development and Highlight Regulatory Aspects of Metabolic Network Behavior1[W] , 2006, Plant Physiology.

[47]  P. Gallusci,et al.  Sucrose deficiency delays lycopene accumulation in tomato fruit pericarp discs , 2006, Plant Molecular Biology.

[48]  K. Bradford,et al.  Galactosyl-sucrose oligosaccharides and potential longevity of primed seeds , 2001, Seed Science Research.

[49]  V. Germain,et al.  Changes in Transcriptional Profiles Are Associated with Early Fruit Tissue Specialization in Tomato1[w] , 2005, Plant Physiology.

[50]  W. Snedden,et al.  Gaba shunt in developing soybean seeds is associated with hypoxia , 1995 .

[51]  T. Fan.  Metabolite profiling by one- and two-dimensional NMR analysis of complex mixtures , 1996 .

[52]  W. Gruissem,et al.  Fruits: A Developmental Perspective. , 1993, The Plant cell.

[53]  P. McCourt,et al.  Fatty acid composition of leaf lipids determined after combined digestion and fatty acid methyl ester formation from fresh tissue. , 1986, Analytical biochemistry.

[54]  P. Minorsky.  TRIGONELLINE: A DIVERSE REGULATOR IN PLANTS , 2002 .

[55]  Robert Verpoorte,et al.  Metabolic Discrimination of Catharanthus roseus Leaves Infected by Phytoplasma Using 1H-NMR Spectroscopy and Multivariate Data Analysis1 , 2004, Plant Physiology.

[56]  Alisdair R. Fernie,et al.  Developmental analysis of carbohydrate metabolism in tomato (Lycopersicon esculentum cv. Micro-Tom) fruits. , 2004, Physiologia plantarum.

[57]  Sébastien Baud,et al.  An integrated overview of seed development in Arabidopsis thaliana ecotype WS , 2002 .

[58]  P. M. Bramley,et al.  Carotenoid Biosynthesis during Tomato Fruit Development (Evidence for Tissue-Specific Gene Expression) , 1994, Plant physiology.

[59]  A. Moing,et al.  Modeling Carbon Export Out of Mature Peach Leaves , 1994, Plant physiology.