Studies of a Biochemical Factory: Tomato Trichome Deep Expressed Sequence Tag Sequencing and Proteomics1[W][OA]

Shotgun proteomics analysis allows hundreds of proteins to be identified and quantified from a single sample at relatively low cost. Extensive DNA sequence information is a prerequisite for shotgun proteomics, and it is ideal to have sequence for the organism being studied rather than from related species or accessions. While this requirement has limited the set of organisms that are candidates for this approach, next generation sequencing technologies make it feasible to obtain deep DNA sequence coverage from any organism. As part of our studies of specialized (secondary) metabolism in tomato (Solanum lycopersicum) trichomes, 454 sequencing of cDNA was combined with shotgun proteomics analyses to obtain in-depth profiles of genes and proteins expressed in leaf and stem glandular trichomes of 3-week-old plants. The expressed sequence tag and proteomics data sets combined with metabolite analysis led to the discovery and characterization of a sesquiterpene synthase that produces β-caryophyllene and α-humulene from E,E-farnesyl diphosphate in trichomes of leaf but not of stem. This analysis demonstrates the utility of combining high-throughput cDNA sequencing with proteomics experiments in a target tissue. These data can be used for dissection of other biochemical processes in these specialized epidermal cells.

[1]  W. Tingey.  Potato Glandular Trichomes: Defensive Activity Against Insect Attack , 1991 .

[2]  H. Yu,et al.  Comparison of polyphenol oxidase expression in glandular trichomes of solanum and lycopersicon species. , 1992, Plant physiology.

[3]  G. Eisenbrand,et al.  Artemisia annua L. , 1992 .

[4]  R. Croteau,et al.  4S-limonene synthase from the oil glands of spearmint (Mentha spicata). cDNA isolation, characterization, and bacterial expression of the catalytically active monoterpene cyclase. , 1993, The Journal of biological chemistry.

[5]  D. Zamir,et al.  An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. , 1995, Genetics.

[6]  A. Shevchenko,et al.  Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. , 1996, Analytical chemistry.

[7]  C. Ryan,et al.  A Gene Encoding a Chloroplast-Targeted Lipoxygenase in Tomato Leaves Is Transiently Induced by Wounding, Systemin, and Methyl Jasmonate , 1997, Plant physiology.

[8]  D. Joel,et al.  Differential Expression and Turnover of the Tomato Polyphenol Oxidase Gene Family during Vegetative and Reproductive Development , 1997, Plant physiology.

[9]  R. Croteau,et al.  Germacrene C synthase from Lycopersicon esculentum cv. VFNT cherry tomato: cDNA isolation, characterization, and bacterial expression of the multiple product sesquiterpene cyclase. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[10]  R. Croteau,et al.  Geranyl diphosphate synthase: cloning, expression, and characterization of this prenyltransferase as a heterodimer. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[11]  X. Huang,et al.  CAP3: A DNA sequence assembly program. , 1999, Genome research.

[12]  B. M. Lange,et al.  Probing essential oil biosynthesis and secretion by functional evaluation of expressed sequence tags from mint glandular trichomes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[13]  R. Van der Hoeven,et al.  Genetic Control and Evolution of Sesquiterpene Biosynthesis in Lycopersicon esculentum and L. hirsutum , 2000, Plant Cell.

[14]  G. Howe,et al.  Cytochrome P450-dependent metabolism of oxylipins in tomato. Cloning and expression of allene oxide synthase and fatty acid hydroperoxide lyase. , 2000, Plant physiology.

[15]  E. Werker.  Trichome diversity and development , 2000 .

[16]  John H. Loughrin,et al.  Suppression of a P450 hydroxylase gene in plant trichome glands enhances natural-product-based aphid resistance , 2001, Nature Biotechnology.

[17]  J. Simon,et al.  An investigation of the storage and biosynthesis of phenylpropenes in sweet basil. , 2001, Plant physiology.

[18]  R. Croteau,et al.  DEFENSIVE RESIN BIOSYNTHESIS IN CONIFERS. , 2003, Annual review of plant physiology and plant molecular biology.

[19]  Anthony L. Schilmiller,et al.  Oxylipin metabolism in response to stress. , 2002, Current opinion in plant biology.

[20]  Alexey I Nesvizhskii,et al.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. , 2002, Analytical chemistry.

[21]  R. Aebersold,et al.  A statistical model for identifying proteins by tandem mass spectrometry. , 2003, Analytical chemistry.

[22]  John Quackenbush,et al.  TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets , 2003, Bioinform..

[23]  E. Pichersky,et al.  Characterization of Geraniol Synthase from the Peltate Glands of Sweet Basil1 , 2004, Plant Physiology.

[24]  D. Grierson,et al.  Identification of a Specific Isoform of Tomato Lipoxygenase (TomloxC) Involved in the Generation of Fatty Acid-Derived Flavor Compounds1 , 2004, Plant Physiology.

[25]  G. Wagner,et al.  New approaches for studying and exploiting an old protuberance, the plant trichome. , 2004, Annals of botany.

[26]  Yuval Eshed,et al.  A genomic library of Lycopersicon pennellii in L. esculentum: A tool for fine mapping of genes , 2004, Euphytica.

[27]  Wolfram Weckwerth,et al.  Cell-specific protein profiling in Arabidopsis thaliana trichomes: identification of trichome-located proteins involved in sulfur metabolism and detoxification. , 2004, Phytochemistry.

[28]  M. Lipton,et al.  Evaluation of two‐dimensional electrophoresis and liquid chromatography – tandem mass spectrometry for tissue‐specific protein profiling of laser‐microdissected plant samples , 2005, Electrophoresis.

[29]  G. Wagner,et al.  Phylloplanins of Tobacco Are Defensive Proteins Deployed on Aerial Surfaces by Short Glandular Trichomes , 2005, The Plant Cell Online.

[30]  J. Ohlrogge,et al.  Metabolic, Genomic, and Biochemical Analyses of Glandular Trichomes from the Wild Tomato Species Lycopersicon hirsutum Identify a Key Enzyme in the Biosynthesis of Methylketonesw⃞ , 2005, The Plant Cell Online.

[31]  J. Vissers,et al.  A proteome approach defines protective functions of tobacco leaf trichomes , 2005, Proteomics.

[32]  B. Haas,et al.  Sequencing Medicago truncatula expressed sequenced tags using 454 Life Sciences technology , 2006, BMC Genomics.

[33]  H. Bouwmeester,et al.  Isoprenoid biosynthesis in Artemisia annua: cloning and heterologous expression of a germacrene A synthase from a glandular trichome cDNA library. , 2006, Archives of biochemistry and biophysics.

[34]  B. Cooper,et al.  Alternative workflows for plant proteomic analysis. , 2006, Molecular bioSystems.

[35]  J. Noel,et al.  Eugenol and isoeugenol, characteristic aromatic constituents of spices, are biosynthesized via reduction of a coniferyl alcohol ester. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[36]  P. Covello,et al.  Artemisia annua L. (Asteraceae) trichome‐specific cDNAs reveal CYP71AV1, a cytochrome P450 with a key role in the biosynthesis of the antimalarial sesquiterpene lactone artemisinin , 2006, FEBS letters.

[37]  M. Washburn,et al.  Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors , 2006, Proceedings of the National Academy of Sciences.

[38]  K. Matsui.  Green leaf volatiles: hydroperoxide lyase pathway of oxylipin metabolism. , 2006, Current opinion in plant biology.

[39]  Douglas J. H. Olson,et al.  Proteomic analysis of tomato (Lycopersicon esculentum) pollen. , 2007, Journal of experimental botany.

[40]  P. Schnable,et al.  Transcriptomic and Proteomic Analyses of Pericycle Cells of the Maize Primary Root , 2007 .

[41]  M. Causse,et al.  Major Proteome Variations Associated with Cherry Tomato Pericarp Development and Ripening[OA] , 2007, Plant Physiology.

[42]  Wei Zhu,et al.  The TIGR Plant Transcript Assemblies database , 2006, Nucleic Acids Res..

[43]  J. Ohlrogge,et al.  Sampling the Arabidopsis Transcriptome with Massively Parallel Pyrosequencing1[W][OA] , 2007, Plant Physiology.

[44]  Sophie Alvarez,et al.  Metabolomic and proteomic changes in the xylem sap of maize under drought. , 2008, Plant, cell & environment.

[45]  S. S. Steiner.  EST Analysis of Hop Glandular Trichomes Identifies an O-Methyltransferase That Catalyzes the Biosynthesis of Xanthohumol , 2008 .

[46]  T. Joshi,et al.  Establishment of a Protein Reference Map for Soybean Root Hair Cells1[W][OA] , 2008, Plant Physiology.

[47]  A. Weber,et al.  Low-coverage massively parallel pyrosequencing of cDNAs enables proteomics in non-model species: comparison of a species-specific database generated by pyrosequencing with databases from related species for proteome analysis of pea chloroplast envelopes. , 2008, Journal of biotechnology.

[48]  D. Gang,et al.  A systems biology investigation of the MEP/terpenoid and shikimate/phenylpropanoid pathways points to multiple levels of metabolic control in sweet basil glandular trichomes. , 2008, The Plant journal : for cell and molecular biology.

[49]  P. Facchini,et al.  Got milk? The secret life of laticifers. , 2008, Trends in plant science.

[50]  B. M. Lange,et al.  A systems biology approach identifies the biochemical mechanisms regulating monoterpenoid essential oil composition in peppermint , 2008, Proceedings of the National Academy of Sciences.

[51]  Yansheng Zhang,et al.  The Molecular Cloning of Artemisinic Aldehyde Δ11(13) Reductase and Its Role in Glandular Trichome-dependent Biosynthesis of Artemisinin in Artemisia annua* , 2008, Journal of Biological Chemistry.

[52]  R. Dixon,et al.  Transcriptomic and Reverse Genetic Analysesof Branched-Chain Fatty Acid and Acyl Sugar Production in Solanum pennellii and Nicotiana benthamiana1[W][OA] , 2008, Plant Physiology.

[53]  R. Verpoorte,et al.  Secondary metabolism in cannabis , 2008, Phytochemistry Reviews.

[54]  Jenny Renaut,et al.  Proteome analysis of non-model plants: a challenging but powerful approach. , 2008, Mass spectrometry reviews.

[55]  Sarah M Assmann,et al.  Functional Proteomics of Arabidopsis thaliana Guard Cells Uncovers New Stomatal Signaling Pathways[W][OA] , 2008, The Plant Cell Online.

[56]  Anthony L. Schilmiller,et al.  Harnessing plant trichome biochemistry for the production of useful compounds. , 2008, The Plant journal : for cell and molecular biology.

[57]  R. Dixon,et al.  Divergent Regulation of Terpenoid Metabolism in the Trichomes of Wild and Cultivated Tomato Species1[W][OA] , 2008, Plant Physiology.

[58]  R. Lister,et al.  Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. , 2009, Current opinion in plant biology.

[59]  Sixue Chen,et al.  Functional Differentiation of Brassica napus Guard Cells and Mesophyll Cells Revealed by Comparative Proteomics*S , 2009, Molecular & Cellular Proteomics.

[60]  D. Schriemer,et al.  Plant Defense Responses in Opium Poppy Cell Cultures Revealed by Liquid Chromatography-Tandem Mass Spectrometry Proteomics*S , 2009, Molecular & Cellular Proteomics.

[61]  Anthony L. Schilmiller,et al.  Monoterpenes in the glandular trichomes of tomato are synthesized from a neryl diphosphate precursor rather than geranyl diphosphate , 2009, Proceedings of the National Academy of Sciences.

[62]  Anthony L. Schilmiller,et al.  Mass spectrometry screening reveals widespread diversity in trichome specialized metabolites of tomato chromosomal substitution lines , 2010, The Plant journal : for cell and molecular biology.

[63]  A. D. Jones,et al.  Distortion of trichome morphology by the hairless mutation of tomato affects leaf surface chemistry , 2009, Journal of experimental botany.

[64]  R. Last,et al.  Shotguns and SNPs: how fast and cheap sequencing is revolutionizing plant biology. , 2010, The Plant journal : for cell and molecular biology.

[65]  A. D. Jones,et al.  Broad connections in the Arabidopsis seed metabolic network revealed by metabolite profiling of an amino acid catabolism mutant. , 2010, The Plant journal : for cell and molecular biology.