Identification of the SAAT gene involved in strawberry flavor biogenesis by use of DNA microarrays

Advances in functional research of antioxidants and organoleptic traits in berry crops

Berry species are economically-important crops worldwide and represent an invaluable source of vitamins and other health-related compounds. Species belonging to the families Rosaceae, Ericaceae and Grossulariaceae provide the most popular fruits, showing a strong diversity in natural and breeding populations as to berry traits (fruit type, size, color, flavor, antioxidant capacity), resistance to a/biotic stress, adaptation to different environment/culture conditions. The small genome size of most diploid berry genera is a remarkable feature for last-generation genomics technologies, molecular genetics and functional studies. This review will cover the literature dealing with molecular research in berry crops, focusing on antioxidant- and flavor-related compounds.

Characterization of major enzymes and genes involved in flavonoid and proanthocyanidin biosynthesis during fruit development in strawberry (Fragaria ×ananassa)

The biosynthesis of flavonoids and proanthocyanidins was studied in cultivated strawberry (Fragaria xananassa) by combining biochemical and molecular approaches. Chemical analyses showed that ripe strawberries accumulate high amounts of pelargonidin-derived anthocyanins, and a larger pool of 3',4'-hydroxylated proanthocyanidins. Activities and properties of major recombinant enzymes were demonstrated by means of in vitro assays, with special emphasis on specificity for the biologically relevant 4'- and 3',4'-hydroxylated compounds. Only leucoanthocyanidin reductase showed a strict specificity for the 3',4'-hydroxylated leucocyanidin, while other enzymes accepted either hydroxylated substrate with different relative activity rates. The structure of late flavonoid pathway genes, leading to the synthesis of major compounds in ripe fruits, was elucidated. Complex developmental and spatial expression patterns were shown for phenylpropanoid and flavonoid genes in fruits throughout ripening as well as in leaves, petals and roots. Presented results elucidate key steps in the biosynthesis of strawberry flavonoid end products.

Gene expression profiling by DNA microarray technology

Methods in molecular and genetic biology have provided important clues to elucidate the complex mechanisms of oral and craniofacial development and pathogenesis of diseases. It has become increasingly clear that a biological phenotype is a result of multiple factors involving a large number of regulatory genes, while a single nucleotide mutation can cause various degrees of oral and craniofacial abnormalities. These oral and craniofacial problems often present a challenge to the molecular screening process. Recent advances in microarray-based technologies allow for large-scale gene expression analysis in a single experiment, which have been applied to genome-wide assays, mutational analysis, drug discovery, developmental biology, and molecular analysis of various diseases. This review introduces the basic principle and some modifications of techniques and materials used in microarray technology, as well as currently available microarray data analysis strategies. Microarray technology can be applied to the soon-to-be-available human genome database and will be a powerful research tool for those inquiring into specific problems associated with oral and craniofacial biology.

Volatile emission after controlled atmosphere storage of Mondial Gala apples (Malus domestica): relationship to some involved enzyme activities

Mondial Gala apples were harvested at commercial maturity and stored at 1 degrees C under either air or controlled atmosphere (CA) conditions (2 kPa O2/2 kPa CO2 and 1 kPa O2/1 kPa CO2), where they remained for 3 or 6 months. Data on emission of selected volatile esters, alcohol precursors, and activity of some aroma-related enzymes in both peel and pulp tissues were obtained during subsequent shelf life of fruit and submitted to multivariate analysis procedures. CA storage caused a decrease in the emission of volatile esters in comparison to storage in air. Results suggest that lessened ester production was the consequence of modifications in activities of alcohol o-acyltransferase (AAT) and lipoxygenase (LOX) activities. For short-term storage, inhibition of lipoxygenase activity in CA stored fruit possibly led to a shortage of lipid-derived substrates, resulting in decreased production of volatile esters in spite of substantial ester-forming capacity that allowed for some recovery of fruit capacity for ester emission during the shelf life. For long-term storage, strong inhibition of AAT activity in CA stored fruit in combination with low LOX activities resulted in unrecoverable diminution of biosynthesis of volatile esters.

Proteomic Variation Is as Large within as between Strawberry Varieties

In search for a strawberry (Fragaria ananassa) with low allergen content, we determined the proteomic variation within and between different varieties. Proteomics data were generated by DIGE and proteins identified with MALDI-MS/MS. The amount of the strawberry allergen Fra a 1 varied between different strawberry varieties (CV = 39%). The variation was at the same level, or even slightly larger, due to different growth conditions (CV = 43%). For 153 other proteins, the biological variation was more affected by different growth conditions than by different varieties (mean CV = 52% and 43%, respectively) due to variation in a subset of proteins. Thus, the allergen variation due to growth conditions must be taken into consideration in attempts to obtain a low-allergen strawberry. However, the allergen content was always lower in colorless (white) strawberry varieties than in the red ones. Moreover, of the spots whose expression correlated with the allergen and the color (32 and 68, respectively), only 3 were the same. This implies that these two phenotypic traits are not inseparable, and it may be possible to breed a red strawberry with low amount of allergen.

Cuticular wax biosynthesis in petunia petals: cloning and characterization of an alcohol-acyltransferase that synthesizes wax-esters

The surface of plants is covered by cuticular wax, which contains a mixture of very long-chain fatty acid (VLCFA) derivatives. This wax surface provides a hydrophobic barrier which reduces non-stomatal water loss. One component of the cuticular wax is the alkyl esters, which typically contain a VLCFA esterified to an alcohol of a similar length. As part of an EST project, we recently identified an acyltransferase with 19% sequence identity (amino acid) to a bacterial 'bifunctional' wax-ester synthase/diacylglycerol acyltransferase (WS/DGAT). Northern analysis revealed that this petunia homologue was expressed predominantly within the petals. The cDNA encoding the WS/DGAT homologue was introduced into a yeast strain deficient in triacylglycerol biosynthesis. The expressed protein failed to restore triacylglycerol biosynthesis, indicating that it lacked DGAT activity. However, isoamyl esters of fatty acids were detected, which suggested that the petunia cDNA encoded a wax-synthase. Waxes were extracted from petunia petals and leaves. The petal wax extract was rich in VLCFA esters of methyl, isoamyl, and short-to-medium straight chain alcohols (C4-C12). These low molecular weight wax-esters were not present in leaf wax. In-vitro enzymes assays were performed using the heterologously expressed protein and 14C-labelled substrates. The expressed protein was membrane bound, and displayed a preference for medium chain alcohols and saturated very long-chain acyl-CoAs. In fact, the activity would be sufficient to produce most of the low molecular wax-esters present in petals, with methyl-esters being the exception. This work is the first characterization of a eukaryotic protein from the WS/DGAT family.

Biochemical and catalytic properties of three recombinant alcohol acyltransferases of melon. sulfur-containing ester formation, regulatory role of CoA-SH in activity, and sequence elements conferring substrate preference

Alcohol acyltransferases (AAT) play a key role in the biosynthesis of ester aroma volatiles in fruit. Three ripening-specific recombinant AATs of cantaloupe Charentais melon fruit (Cm-AAT1, Cm-AAT3, and Cm-AAT4) are capable of synthesizing thioether esters with Cm-AAT1 being by far the most active. All proteins, as well as AAT(s) extracted from melon fruit, are active as tetramers of around 200 kDa. Kinetic analysis demonstrated that CoA-SH, a product of the reaction, is an activator at low concentrations and an inhibitor at higher concentrations. This was confirmed by the addition of phosphotransacetylase at various concentrations, capable of modulating the level of CoA-SH in the reaction medium. Site-directed mutagenesis of some amino acids that were specific to the Cm-AAT sequences into amino acids that were consensus to other characterized AATs greatly affected the selectivity of the original protein and the number of esters produced.

Prokaryotic expression, purification, and sub-cellular localization of a novel alcohol acyltransferase from apple

The coding region of the alcohol acyltransferase gene (MdAAT2) from apple was sub-cloned into expression vectors, pET30a and pET32a, and introduced into E. coli for expression. The purified pET30a/MdAAT2 fusion proteins were used to immunize rabbits following standard protocols. The partially soluble fusion proteins had alcohol acyltransferase activity and were detected only in the pET32a/Origami B(DE3) expression system. Immunolocalization analysis indicated that MdAAT2 is mainly in the cytoplasm, in agreement with the prediction of sub-cellular localization obtained by the LOCSVMpsi program. Western blot analysis indicated that ester biosynthesis in different apple cultivars was related positively to the accumulation of MdAAT2.

Pathway analysis of branched-chain ester biosynthesis in apple using deuterium labeling and enantioselective gas chromatography-mass spectrometry

The biosynthesis of volatile esters by Red Delicious apples was investigated by incubating fruit tissue with deuterated flavor precursors at various times after controlled atmosphere (CA) storage and measuring deuterium incorporation into branched-chain ester volatiles. 2-Methylbutyl acetate was the only volatile not significantly reduced by CA storage. Conversion of 2-methylbutanol to 2-methylbutyl acetate and of 2-methylbutanoic acid to ethyl 2-methylbutanoate and to hexyl 2-methylbutanoate was limited by the availability of 2-methylbutyl substrates but not by acetyl-CoA, ethanol, or hexanol, respectively. The enzymatic activity required for these reactions declined during CA storage. The conversion of 2-methylbutanoic acid to 2-methylbutanol was also substrate limited, but enzymic activity appeared stable in storage. Biosynthesis of both 2-methylbutanoic acid and 2-methylbutanol, from isoleucine, was severely depressed under CA storage. The reduced metabolism of isoleucine to 2-methylbutanoyl-CoA may be the primary reason for reduced branched-chain ester synthesis in CA-stored Red Delicious apples. Enantioselective gas chromatography-mass spectrometry confirmed that the chirality of (S)-2-methylbutyl acetate derives from l-isoleucine with the other enzymes in this pathway not being enantiospecific. Treatment of tissue samples with 2-methylbut-2E-enal gave only (S)-2-methylbutyl acetate, indicating that biosynthesis was not via tiglyl-CoA.

Genetic aspects of floral fragrance in plants

It is generally assumed that compounds are emitted from flowers in order to attract and guide pollinators. Due to the invisibility and the highly variable nature of floral scent, no efficient and reliable methods to screen for genetic variation have been developed. Moreover, no convenient plant model systems are available for flower scent studies. In the past decade, several floral fragrance-related genes have been cloned; the biosynthesis and metabolic engineering of floral volatiles have been studied with the development of biotechnology. This review summarizes the reported floral fragrance-related genes and the biosynthesis of floral scent compounds, introduces the origin of new modification enzymes for flower scent, compares different methods for floral fragrance-related gene cloning, and discusses the metabolic engineering of floral scent. Finally, the perspectives and prospects of research on floral fragrance are presented.

Expression of plant flavor genes in Lactococcus lactis

Lactic acid bacteria, such as Lactococcus lactis, are attractive hosts for the production of plant-bioactive compounds because of their food grade status, efficient expression, and metabolic engineering tools. Two genes from strawberry (Fragaria x ananassa), encoding an alcohol acyltransferase (SAAT) and a linalool/nerolidol synthase (FaNES), were cloned in L. lactis and actively expressed using the nisin-induced expression system. The specific activity of SAAT could be improved threefold (up to 564 pmol octyl acetate h-1 mg protein-1) by increasing the concentration of tRNA1Arg, which is a rare tRNA molecule in L. lactis. Fermentation tests with GM17 medium and milk with recombinant L. lactis strains expressing SAAT or FaNES resulted in the production of octyl acetate (1.9 microM) and linalool (85 nM) to levels above their odor thresholds in water. The results illustrate the potential of the application of L. lactis as a food grade expression platform for the recombinant production of proteins and bioactive compounds from plants.

RNAi-induced silencing of gene expression in strawberry fruit (Fragaria x ananassa) by agroinfiltration: a rapid assay for gene function analysis

Intron-containing constructs encoding self-complementary 'hairpin' RNA (ihpRNA) have the potential to efficiently silence genes in a range of plant species. In this study we demonstrate the silencing of a ripening-related chalcone synthase (CHS) gene in strawberry fruits (Fragaria x ananassa cv. Elsanta) by a construct (ihpRNA) containing the partial sense and corresponding antisense sequences of CHS separated by an intron obtained from a F. x ananassa quinone oxidoreductase gene. An Agrobacterium strain carrying a T-DNA expressing the ihpRNA transgene was injected with a syringe into the receptacles of growing fruits still attached to the plant about 14 days after pollination. As a consequence of the reduced levels of CHS mRNA and enzymatic CHS activity, the levels of anthocyanins were downregulated and precursors of the flavonoid pathway were shunted to the phenylpropanoid pathway leading to a large increases in levels of (hydroxy) cinnamoyl glucose esters. We anticipate that this technique in combination with metabolite profiling analysis will be useful for studying the function of unknown genes during the development and ripening of strawberry fruit.

The role of profilin and lipid transfer protein in strawberry allergy in the Mediterranean area

BACKGROUND

In contrast to other Rosaceae fruit, only few cases of patients with adverse reactions to strawberry are listed in literature. OBJECTIVE To identify allergenic proteins in strawberry and to express and characterize recombinant strawberry lipid transfer protein (LTP; rFra a 3).

METHODS

Established apple-allergic patients were recruited on the basis of a reported allergic reaction to strawberry (n=28, confirmed by double-blind placebo-controlled food challenge in four patients) or on the basis of IgE reactivity to LTP (n=34). Sensitization to purified natural and recombinant allergens was assessed by RAST, immunoblot (inhibition) and basophil histamine release (BHR). A strawberry cDNA library was screened for genes homologous to known fruit allergens. Fra a 3 was cloned and expressed in the yeast Pichia pastoris and compared with peach and apple LTP by RAST, immunoblot-inhibition and BHR tests.

RESULTS

Genes homologous to Bet v 1, Bet v 6, profilin and LTP were identified in a strawberry cDNA library. In BHR the rFra a 3 induced histamine release at a 100-fold higher concentration than peach LTP. RAST inhibition showed high cross-reactivity to peach and apple LTP, although IgE reactivity was lower by a factor 5. On strawberry immunoblot, patients' IgE showed reactivity to a Bet v 1 homologue, profilin, LTP and high-molecular weight bands.

CONCLUSION

In addition to a Bet v 1 homologue, strawberry also contains IgE-binding profilin and LTP. The rFra a 3 has less allergenic potency than peach and apple LTP, and therefore is an interesting tool for future immunotherapy. Fra a 3 does not seem to be clinically relevant.

Characterization of LF9, an octoploid strawberry genotype selected for rapid regeneration and transformation

Cultivated strawberry (Fragaria xananassa) is a valuable crop, yet the absence of a rapid, high-throughput transgenic system has precluded meaningful application of biotechnology and translation of information from plant models to this crop. A new octoploid strawberry genetic line Laboratory Festival #9 has been identified, selected solely for its rapid regeneration and efficient transformation. Direct organogenesis has been achieved from all tissues tested, with rapidly-growing shoot initials visible in as few as 13 days. The conditions for optimal shoot regeneration, transformant selection, root generation, and plant acclimatization are presented. The progression from explant to plant in soil can be achieved in about 60 days. The development of transformation protocols in this rapid-cycling genotype allows high-throughput studies of gene function in the octoploid strawberry genetic background.

Acyltransferases in plants: a good time to be BAHD

Acylation is a common and biochemically significant modification of plant secondary metabolites. Plant BAHD acyltransferases constitute a large family of acyl CoA-utilizing enzymes whose products include small volatile esters, modified anthocyanins, as well as constitutive defense compounds and phytoalexins. The catalytic versatility of BAHD enzymes makes it very difficult to make functional predictions from primary sequence alone. Recent advances in genome sequencing and the availability of the first crystal structure of a BAHD member are, however, providing insights into the evolution and function of these acyltransferases within the plant kingdom.

Salicylic acid, ethephon, and methyl jasmonate enhance ester regeneration in 1-MCP-treated apple fruit after long-term cold storage

Volatile esters, primarily synthesized in peel tissues, are major aromatic components of apple fruits [Malus sylvestris (L.) Mill. var. domestica (Borkh.) Mansf.]. The use of cold storage combined with 1-methylcyclopropene (1-MCP) treatment prolongs the life of apples but represses the regeneration of esters during poststorage ripening. In this study, the regeneration of total esters was significantly increased in apple fruits treated with salicylic acid (SA) and Ethephon (ETH) that had been treated once or twice with 1-MCP. However, methyl jasmonate (MeJA) treatment resulted in regeneration of total esters after a single 1-MCP treatment. To determine the mechanism by which SA, ETH, and MeJA regulate ester regeneration, the apple alcohol acyltransferase gene (MdAAT2) was investigated at the mRNA, protein, and enzyme activity levels. Genes associated with ethylene perception were also investigated by RT-PCR. The results suggest that MdAAT2 controls ester regeneration and that MdETR1 plays a key role in ethylene perception and regulation of downstream MdAAT2 gene expression during poststorage. Ester compounds and concentrations differed in peels treated with different signal molecules, indicating that regulation of the pathway upstream of straight-chain ester biosynthesis depended on the regulation of lipoxygenase (LOX) and alcohol dehydrogenase (ADH) activity by SA, ETH, and MeJA during poststorage ripening.

Analyses of expressed sequence tags from apple

The domestic apple (Malus domestica; also known as Malus pumila Mill.) has become a model fruit crop in which to study commercial traits such as disease and pest resistance, grafting, and flavor and health compound biosynthesis. To speed the discovery of genes involved in these traits, develop markers to map genes, and breed new cultivars, we have produced a substantial expressed sequence tag collection from various tissues of apple, focusing on fruit tissues of the cultivar Royal Gala. Over 150,000 expressed sequence tags have been collected from 43 different cDNA libraries representing 34 different tissues and treatments. Clustering of these sequences results in a set of 42,938 nonredundant sequences comprising 17,460 tentative contigs and 25,478 singletons, together representing what we predict are approximately one-half the expressed genes from apple. Many potential molecular markers are abundant in the apple transcripts. Dinucleotide repeats are found in 4,018 nonredundant sequences, mainly in the 5'-untranslated region of the gene, with a bias toward one repeat type (containing AG, 88%) and against another (repeats containing CG, 0.1%). Trinucleotide repeats are most common in the predicted coding regions and do not show a similar degree of sequence bias in their representation. Bi-allelic single-nucleotide polymorphisms are highly abundant with one found, on average, every 706 bp of transcribed DNA. Predictions of the numbers of representatives from protein families indicate the presence of many genes involved in disease resistance and the biosynthesis of flavor and health-associated compounds. Comparisons of some of these gene families with Arabidopsis (Arabidopsis thaliana) suggest instances where there have been duplications in the lineages leading to apple of biosynthetic and regulatory genes that are expressed in fruit. This resource paves the way for a concerted functional genomics effort in this important temperate fruit crop.

FaQR, required for the biosynthesis of the strawberry flavor compound 4-hydroxy-2,5-dimethyl-3(2H)-furanone, encodes an enone oxidoreductase

The flavor of strawberry (Fragaria x ananassa) fruit is dominated by an uncommon group of aroma compounds with a 2,5-dimethyl-3(H)-furanone structure. We report the characterization of an enzyme involved in the biosynthesis of 4-hydroxy-2,5-dimethyl-3(2H)-furanone (HDMF; Furaneol), the key flavor compound in strawberries. Protein extracts were partially purified, and the observed distribution of enzymatic activity correlated with the presence of a single polypeptide of approximately 37 kD. Sequence analysis of two peptide fragments showed total identity with the protein sequence of a strongly ripening-induced, auxin-dependent putative quinone oxidoreductase, Fragaria x ananassa quinone oxidoreductase (FaQR). The open reading frame of the FaQR cDNA consists of 969 bp encoding a 322-amino acid protein with a calculated molecular mass of 34.3 kD. Laser capture microdissection followed by RNA extraction and amplification demonstrated the presence of FaQR mRNA in parenchyma tissue of the strawberry fruit. The FaQR protein was functionally expressed in Escherichia coli, and the monomer catalyzed the formation of HDMF. After chemical synthesis and liquid chromatography-tandem mass spectrometry analysis, 4-hydroxy-5-methyl-2-methylene-3(2H)-furanone was confirmed as a substrate of FaQR and the natural precursor of HDMF. This study demonstrates the function of the FaQR enzyme in the biosynthesis of HDMF as enone oxidoreductase and provides a foundation for the improvement of strawberry flavor and the biotechnological production of HDMF.

Molecular characterization of a stable antisense chalcone synthase phenotype in strawberry (Fragaria x ananassa)

An octaploid (Fragaria x ananassa cv. Calypso) genotype of strawberry was transformed with an antisense chalcone synthase (CHS) gene construct using a ripening related CHS cDNA from Fragaria x ananassa cv. Elsanta under the control of the constitutive CaMV 35S promoter via Agrobacterium tumefaciens. Out of 25 transgenic lines, nine lines showed a reduction in CHS mRNA accumulation of more than 50% as compared to the untransformed cv. Calypso control. The antisense CHS construct was found to be integrated into the genome, with a copy number ranging from one to four. The pigmentation of the fruit was only affected when less than 5% of the control CHS expression level was detected. A stable antisense phenotype over a period of 4 years was obtained in the primary transgenic lines at a rate of 1:20. As a consequence of the reduced activity of CHS, the levels of anthocyanins, flavonols, and proanthocyanidins were downregulated and precursors of the flavonoid pathway were shunted to the phenylpropanoid pathway leading to highly increased levels of cinnamoyl glucose (520% of control), caffeoyl glucose (816% of control), and feruloyl glucose (1092% of control) as well as p-coumaryl alcohol (363% of control) and p-coumaryl-1-acetate (1079% of control), which occur only as trace components in untransformed control fruits. These results demonstrate that the introduction of an antisense CHS construct in strawberry results in an unpredictable biochemical phenotype, thereby confirming that CHS function is an important regulatory point of substrate flow between the flavonoid and the phenylpropanoid pathways.

Generation of phenylpropanoid pathway-derived volatiles in transgenic plants: rose alcohol acetyltransferase produces phenylethyl acetate and benzyl acetate in petunia flowers

Esters are important contributors to the aroma of numerous flowers and fruits. Acetate esters such as geranyl acetate, phenylethyl acetate and benzyl acetate are generated as a result of the action of alcohol acetyltransferases (AATs). Numerous homologous AATs from various plants have been characterized using in-vitro assays. To study the function of rose alcohol acetyltransferase (RhAAT) in planta, we generated transgenic petunia plants expressing the rose gene under the control of a CaMV-35S promoter. Although the preferred substrate of RhAAT in vitro is geraniol, in transgenic petunia flowers, it used phenylethyl alcohol and benzyl alcohol to produce the corresponding acetate esters, not generated by control flowers. The level of benzyl alcohol emitted by the flowers of different transgenic lines was ca. three times higher than that of phenylethyl alcohol, which corresponded to the ratio between the respective products, i.e. ca. three times more benzyl acetate than phenylethyl acetate. Feeding of transgenic petunia tissues with geraniol or octanol led to the production of their respective acetates, suggesting the dependence of volatile production on substrate availability.

Cinnamate metabolism in ripening fruit. Characterization of a UDP-glucose:cinnamate glucosyltransferase from strawberry

Strawberry (Fragaria x ananassa) fruit accumulate (hydroxy)cinnamoyl glucose (Glc) esters, which may serve as the biogenetic precursors of diverse secondary metabolites, such as the flavor constituents methyl cinnamate and ethyl cinnamate. Here, we report on the isolation of a cDNA encoding a UDP-Glc:cinnamate glucosyltransferase (Fragaria x ananassa glucosyltransferase 2 [FaGT2]) from ripe strawberry cv Elsanta that catalyzes the formation of 1-O-acyl-Glc esters of cinnamic acid, benzoic acid, and their derivatives in vitro. Quantitative real-time PCR analysis indicated that FaGT2 transcripts accumulate to high levels during strawberry fruit ripening and to lower levels in flowers. The levels in fruits positively correlated with the in planta concentration of cinnamoyl, p-coumaroyl, and caffeoyl Glc. In the leaf, high amounts of Glc esters were detected, but FaGT2 mRNA was not observed. The expression of FaGT2 is negatively regulated by auxin, induced by oxidative stress, and by hydroxycinnamic acids. Although FaGT2 glucosylates a number of aromatic acids in vitro, quantitative analysis in transgenic lines containing an antisense construct of FaGT2 under the control of the constitutive 35S cauliflower mosaic virus promoter demonstrated that the enzyme is only involved in the formation of cinnamoyl Glc and p-coumaroyl Glc during ripening.

Identification of loci affecting flavour volatile emissions in tomato fruits

Fresh tomato fruit flavour is the sum of the interaction between sugars, acids, and a set of approximately 30 volatile compounds synthesized from a diverse set of precursors, including amino acids, lipids, and carotenoids. Some of these volatiles impart desirable qualities while others are negatively perceived. As a first step to identify the genes responsible for the synthesis of flavour-related chemicals, an attempt was made to identify loci that influence the chemical composition of ripe fruits. A genetically diverse but well-defined Solanum pennellii IL population was used. Because S. pennellii is a small green-fruited species, this population exhibits great biochemical diversity and is a rich source of genes affecting both fruit development and chemical composition. This population was used to identify multiple loci affecting the composition of chemicals related to flavour. Twenty-five loci were identified that are significantly altered in one or more of 23 different volatiles and four were altered in citric acid content. It was further shown that emissions of carotenoid-derived volatiles were directly correlated with the fruit carotenoid content. Linked molecular markers should be useful for breeding programmes aimed at improving fruit flavour. In the longer term, the genes responsible for controlling the levels of these chemicals will be important tools for understanding the complex interactions that ultimately integrate to provide the unique flavour of a tomato.

Isogene specific oligo arrays reveal multifaceted changes in gene expression during grape berry (Vitis vinifera L.) development

The transition from a green, hard, and acidic pericarp to a sweet, soft, coloured, and sugar-rich ripe fruit occurs in many unrelated fruit species. High throughput identification of differentially expressed genes in grape berry has been achieved by the use of 50-mers oligoarrays bearing a set of 3,200 Unigenes from Vitis vinifera to compare berry transcriptome at nine developmental stages. Analysis of transcript profiles revealed that most activations were triggered simultaneously with softening, occurring within only 24 h for an individual berry, just before any change in colouration or water, sugar, and acid content can be detected. Although most dramatically induced genes belong to unknown functional categories, numerous changes occur in the expression of isogenes involved in primary and secondary metabolism during ripening. Focusing on isogenes potentially significant in development regulation (hormonal control of transcription factor) revealed a possible role for several hormones (cytokinin, gibberellin, or jasmonic acid). Transcription factor analysis revealed the induction of RAP2 and WRKY genes at véraison, suggesting increasing biotic and abiotic stress conditions during ripening. This observation was strengthened by an increased expression of multiple transcripts involved in sugar metabolism and also described as induced in other plant organs during stress conditions. This approach permitted the identification of new isogenes as possible control points: a glutathione S-transferase exhibits the same expression profile as anthocyanin accumulation and a new putative sugar transporter is induced in parallel with sugar import.

The biosynthesis and regulation of biosynthesis of Concord grape fruit esters, including 'foxy' methylanthranilate

The biosynthesis of methyl anthranilate, the volatile compound responsible for the distinctive 'foxy' aroma and flavor of the Washington Concord grape (Vitis labrusca), involves an alcohol acyltransferase that catalyzes the formation of methyl anthranilate from anthraniloyl-coenzyme A (CoA) and methanol. Although methanol is a poor substrate in comparison with the co-substrate, high levels of this acyltransferase (0.5% of the total protein) combined with relatively high levels of this alcohol make this reaction possible in grapes. This 449 amino acid protein belongs to the BAHD family of acyltransferases, having 58% identity with the benzoyl CoA:benzyl alcohol benzoyl transferase from Clarkia. Both native and recombinant enzymes can use a broad range of acyl-CoAs and alcohols as substrates. The ability of Concord grape alcohol acyltransferase to accept a range of different CoA esters and alcohols suggests this to be a versatile ester-forming enzyme, similar to those of other fruits that than can produce a range of fruit esters based on the supply of appropriate substrates. Expression is coordinately regulated, with transcript, protein and enzyme activities coinciding with the accumulation of methyl anthranilate that occurs after the initiation of berry ripening. The majority of acyltransferase protein in grape tissues is localized to the outer fruit mesocarp, a result consistent with the fact that methyl anthranilate is released to the external environment throughout the ripening process. Wine grapes (Vitis vinifera) that accumulate neither anthranilate nor methyl anthranilate do not express this enzyme activity nor do they accumulate this protein.

Developmental and varietal differences in volatile ester formation and acetyl-CoA: alcohol acetyl transferase activities in apple (Malus domestica Borkh.) fruit

Apple (Malus domestica Borkh.) cultivars differ in their aroma and composition of volatile acetates in their fruit flesh and peel. Cv. Fuji flesh contains substantial levels of 2-methyl butyl acetate (fruity banana-like odor), while the flesh of cv. Granny Smith apples lacks this compound. Granny Smith apples accumulate mainly hexyl acetate (apple-pear odor) in their peel. Feeding experiments indicated that Fuji apples were able to convert hexanol and 2-methyl butanol to their respective acetate derivatives in vivo, while Granny Smith apples could only convert exogenous hexanol to hexyl acetate. Differential substrate specificities of the in vitro acetyl-CoA:alcohol acetyl transferase (AAT) activities were also detected among cultivars. In Granny Smith apples, the AAT activity was detected only in the peel, and its specificity was almost exclusively restricted to hexanol and cis-3-hexenol. In Fuji apples, the AAT activity was detected in both peel and flesh and apparently accepted a broader range of alcohols as substrates than the Granny Smith enzyme activity. Our data strongly suggest that different AAT activities are operational in apple tissues and cultivars and that these differences contribute to the variation observed in the accumulation of volatile acetates.

Functional characterization of a melon alcohol acyl-transferase gene family involved in the biosynthesis of ester volatiles. Identification of the crucial role of a threonine residue for enzyme activity*

Volatile esters, a major class of compounds contributing to the aroma of many fruit, are synthesized by alcohol acyl-transferases (AAT). We demonstrate here that, in Charentais melon (Cucumis melo var. cantalupensis), AAT are encoded by a gene family of at least four members with amino acid identity ranging from 84% (Cm-AAT1/Cm-AAT2) and 58% (Cm-AAT1/Cm-AAT3) to only 22% (Cm-AAT1/Cm-AAT4). All encoded proteins, except Cm-AAT2, were enzymatically active upon expression in yeast and show differential substrate preferences. Cm-AAT1 protein produces a wide range of short and long-chain acyl esters but has strong preference for the formation of E-2-hexenyl acetate and hexyl hexanoate. Cm-AAT3 also accepts a wide range of substrates but with very strong preference for producing benzyl acetate. Cm-AAT4 is almost exclusively devoted to the formation of acetates, with strong preference for cinnamoyl acetate. Site directed mutagenesis demonstrated that the failure of Cm-AAT2 to produce volatile esters is related to the presence of a 268-alanine residue instead of threonine as in all active AAT proteins. Mutating 268-A into 268-T of Cm-AAT2 restored enzyme activity, while mutating 268-T into 268-A abolished activity of Cm-AAT1. Activities of all three proteins measured with the prefered substrates sharply increase during fruit ripening. The expression of all Cm-AAT genes is up-regulated during ripening and inhibited in antisense ACC oxidase melons and in fruit treated with the ethylene antagonist 1-methylcyclopropene (1-MCP), indicating a positive regulation by ethylene. The data presented in this work suggest that the multiplicity of AAT genes accounts for the great diversity of esters formed in melon.

Integrating genomics and metabolomics for engineering plant metabolic pathways

Plant metabolites are characterized by an enormous chemical diversity, every plant having its own complex set of metabolites. This variety poses analytical challenges, both for profiling multiple metabolites in parallel and for the quantitative analysis of selected metabolites. We are only just starting to understand the roles of these metabolites, many of them being involved in adaptations to specific ecological niches and some finding beneficial use (e.g. as pharmaceuticals). Spectacular advances in plant metabolomics offer new possibilities, together with the aid of systems biology, to explore the extraordinary complexity of the plant biochemical capacity. State-of-the art genomics tools can be combined with metabolic profiling to identify key genes that could be engineered for the production of improved crop plants.

Volatile profiling of Arabidopsis thaliana - putative olfactory compounds in plant communication

Arabidopsis thaliana from the Brassicaceae family has arisen as the model organism in plant biology research. The plant's genome has been characterized and worldwide studies are conducted at the genetic, protein and metabolic level to unravell the function of genes involved in growth, reproduction, biosynthesis, and plant communication. As part of the multidisciplinary project BIOEMIT at NTNU, metabolomic studies of Arabidopsis T-DNA knock-out mutants and ecotypes have been carried out. Volatile profiles of autolyzed, intact plants and single plant organs were obtained by solid-phase microextraction coupled with gas chromatography-mass spectrometry. The studies were aimed at the diversity of defense-related compounds from the glucosinolate-myrosinase system - the isothiocyanates and nitriles. Metabolites from methionine, leucine and phenylalanine-derived glucosinolates were most abundant (4-methylthiobutyl, 4-methylpentyl, 2-phenylethyl). In addition, 24 monoterpenes, 26 sesquiterpenes and 12 aromatic structures, predominantly observed in inflorescenses, are described. Excluding the vast group of straight chain aliphatic structures, a total of 102 volatile compounds were detected, of which 59 are reported in Arabidopsis thaliana for the first time, thus emphasizing the sensitivity and applicability of solid-phase microextraction for volatile profiling of plant secondary metabolites.

Elucidation of Gene-to-Gene and Metabolite-to-Gene Networks inArabidopsis by Integration of Metabolomics andTranscriptomics

Since the completion of genome sequences of model organisms, functional identification of unknown genes has become a principal challenge in biology. Post-genomics sciences such as transcriptomics, proteomics, and metabolomics are expected to discover gene functions. This report outlines the elucidation of gene-to-gene and metabolite-to-gene networks via integration of metabolomics with transcriptomics and presents a strategy for the identification of novel gene functions. Metabolomics and transcriptomics data of Arabidopsis grown under sulfur deficiency were combined and analyzed by batch-learning self-organizing mapping. A group of metabolites/genes regulated by the same mechanism clustered together. The metabolism of glucosinolates was shown to be coordinately regulated. Three uncharacterized putative sulfotransferase genes clustering together with known glucosinolate biosynthesis genes were candidates for involvement in biosynthesis. In vitro enzymatic assays of the recombinant gene products confirmed their functions as desulfoglucosinolate sulfotransferases. Several genes involved in sulfur assimilation clustered with O-acetylserine, which is considered a positive regulator of these genes. The genes involved in anthocyanin biosynthesis clustered with the gene encoding a transcriptional factor that up-regulates specifically anthocyanin biosynthesis genes. These results suggested that regulatory metabolites and transcriptional factor genes can be identified by this approach, based on the assumption that they cluster with the downstream genes they regulate. This strategy is applicable not only to plant but also to other organisms for functional elucidation of unknown genes.

Expressed sequence tags (ESTs) and simple sequence repeat (SSR) markers from octoploid strawberry (Fragaria x ananassa)

BACKGROUND

Cultivated strawberry (Fragaria x ananassa) represents one of the most valued fruit crops in the United States. Despite its economic importance, the octoploid genome presents a formidable barrier to efficient study of genome structure and molecular mechanisms that underlie agriculturally-relevant traits. Many potentially fruitful research avenues, especially large-scale gene expression surveys and development of molecular genetic markers have been limited by a lack of sequence information in public databases. As a first step to remedy this discrepancy a cDNA library has been developed from salicylate-treated, whole-plant tissues and over 1800 expressed sequence tags (EST's) have been sequenced and analyzed.

RESULTS

A putative unigene set of 1304 sequences--133 contigs and 1171 singlets--has been developed, and the transcripts have been functionally annotated. Homology searches indicate that 89.5% of sequences share significant similarity to known/putative proteins or Rosaceae ESTs. The ESTs have been functionally characterized and genes relevant to specific physiological processes of economic importance have been identified. A set of tools useful for SSR development and mapping is presented.

CONCLUSION

Sequences derived from this effort may be used to speed gene discovery efforts in Fragaria and the Rosaceae in general and also open avenues of comparative mapping. This report represents a first step in expanding molecular-genetic analyses in strawberry and demonstrates how computational tools can be used to optimally mine a large body of useful information from a relatively small data set.

An alcohol acyl transferase from apple (cv. Royal Gala), MpAAT1, produces esters involved in apple fruit flavor

Apple flavor is characterized by combinations of ester compounds, which increase markedly during fruit ripening. The final step in ester biosynthesis is catalyzed by alcohol acyl transferases (AATs) that use coenzyme A (CoA) donors together with alcohol acceptors as substrates. The gene MpAAT1, which produces a predicted protein containing features of other plant acyl transferases, was isolated from Malus pumila (cv. Royal Gala). The MpAAT1 gene is expressed in leaves, flowers and fruit of apple. The recombinant enzyme can utilize a range of alcohol substrates from short to medium straight chain (C3-C10), branched chain, aromatic and terpene alcohols. The enzyme can also utilize a range of short to medium chain CoAs. The binding of the alcohol substrate is rate limiting compared with the binding of the CoA substrate. Among different alcohol substrates there is more variation in turnover compared with K(m) values. MpAAT1 is capable of producing many esters found in Royal Gala fruit, including hexyl esters, butyl acetate and 2-methylbutyl acetate. Of these, MpAAT1 prefers to produce the hexyl esters of C3, C6 and C8 CoAs. For the acetate esters, however, MpAAT1 preference depends upon substrate concentration. At low concentrations of alcohol substrate the enzyme prefers utilizing the 2-methylbutanol over hexanol and butanol, while at high concentrations of substrate hexanol can be used at a greater rate than 2-methylbutanol and butanol. Such kinetic characteristics of AATs may therefore be another important factor in understanding how the distinct flavor profiles of different fruit are produced during ripening.

The biotin-streptavidin interaction can be reversibly broken using water at elevated temperatures

The biotin-streptavidin system is the strongest noncovalent biological interaction known, having a dissociation constant, K(d), in the order of 4x10(-14) M. The strength and specificity of the interaction has led it to be one of the most widely used affinity pairs in molecular, immunological, and cellular assays. However, it has previously been impossible to re-use any streptavidin solid support, since the conditions needed to break the interaction with biotin has led to the denaturation of the streptavidin. Here, we show that a short incubation in nonionic aqueous solutions at temperatures above 70 degrees C can efficiently break the interaction without denaturing the streptavidin tetramer. Both biotin and the streptavidin remain active after dissociation and both molecules can therefore be re-used. The efficiency of the regeneration allowed solid supports with streptavidin to be used many times, here exemplified with the multiple re-use of streptavidin beads used for sample preparation prior to automated DNA sequencing. The results suggest that streptavidin regeneration can be introduced as an improvement in existing methods and assays based on the streptavidin system as well as emerging solid phase applications in fields, such as microfluidics and nanotechnology.

New insights into the complex and coordinated transcriptional regulation networks underlying rice seed development through cDNA chip-based analysis

Transcription factors (TFs) are major, crucial factors for developmental control. To elucidate the effects of TFs on rice seed development, we generated a cDNA chip containing 325 rice cDNA clones, which are from flowering stage and encode known or putative TFs belonging to 12 different families, and used this chip for expression profiling at 8 continuous seed developmental stages. The results showed that in comparison to their expression in mature leaves, a total of 135 TF genes were preferentially transcribed in seeds. Cluster analysis based on the temporal expression patterns grouped them into 12 types, each of which contained members of various families showing common unique expression patterns. The results provide insights into possible key roles for members of several TF families during seed development. In addition, the expression patterns of these genes were examined in vegetative tissues including roots, seedlings and stems, as well as in 2-week-old seedlings following the application of plant hormones or abiotic stresses. The results showed that many of the seed-preferential TFs were also involved in hormone and/or abiotic stress effects, suggesting the potential existence of uncharacterized transcriptional networks, or cross talk between hormone and abiotic stress signaling and seed development. Furthermore, analysis on the cis-elements locating in promoter region of seed preferential TF genes suggested that Dof proteins play essential roles in hierarchical regulation of gene expressions during rice seed development, which, taken together, provided informative clues for elucidation of the molecular mechanisms of transcriptional regulation and signaling networks in the complex developmental processes of rice seeds.

Diversifying carotenoid biosynthetic pathways by directed evolution

Microorganisms and plants synthesize a diverse array of natural products, many of which have proven indispensable to human health and well-being. Although many thousands of these have been characterized, the space of possible natural products--those that could be made biosynthetically--remains largely unexplored. For decades, this space has largely been the domain of chemists, who have synthesized scores of natural product analogs and have found many with improved or novel functions. New natural products have also been made in recombinant organisms, via engineered biosynthetic pathways. Recently, methods inspired by natural evolution have begun to be applied to the search for new natural products. These methods force pathways to evolve in convenient laboratory organisms, where the products of new pathways can be identified and characterized in high-throughput screening programs. Carotenoid biosynthetic pathways have served as a convenient experimental system with which to demonstrate these ideas. Researchers have mixed, matched, and mutated carotenoid biosynthetic enzymes and screened libraries of these "evolved" pathways for the emergence of new carotenoid products. This has led to dozens of new pathway products not previously known to be made by the assembled enzymes. These new products include whole families of carotenoids built from backbones not found in nature. This review details the strategies and specific methods that have been employed to generate new carotenoid biosynthetic pathways in the laboratory. The potential application of laboratory evolution to other biosynthetic pathways is also discussed.

Gene expression profile in response to Xanthomonas axonopodis pv. manihotis infection in cassava using a cDNA microarray

A cassava cDNA microarray based on a large cassava EST database was constructed and used to study the incompatible interaction between cassava and Xanthomonas axonopodis pv. manihotis (Xam) strain CIO151. For microarray construction, 5700 clones from the cassava unigene set were amplified by polymerase chain reaction (PCR) and printed on glass slides. Microarray hybridization was performed using cDNA from cassava plants (resistant variety MBra685) collected at 12, 24, 48 h and 7 and 15 days post-infection as treatment and cDNA from mock-inoculated plants as control. A total of 199 genes were found to be differentially expressed (126 up-regulated and 73 down-regulated). A greater proportion of differentially-expressed genes was observed at 7 days after inoculation. Expression profiling and cluster analyses indicate that, in response to inoculation with Xam, cassava induces dozens of genes, including principally those involved in oxidative burst, protein degradation and pathogenesis-related (PR) genes. In contrast, genes encoding proteins that are involved in photosynthesis and metabolism were down regulated. In addition, various other genes encoding proteins with unknown function or showing no similarity to other proteins were also induced. Quantitative real time PCR experiments confirmed the reliability of our microarray data. In addition we showed that some genes are induced more rapidly in the resistant than in the susceptible cultivar.

Antioxidant metabolite profiles in tomato fruit constitutively expressing the grapevine stilbene synthase gene

Tomato (Lycopersicon esculentum Mill.) tissues were transformed with a grape (Vitis vinifera L.) stilbene synthase cDNA, transcriptionally regulated by the cauliflower mosaic virus (CaMV) 35S promoter. Transgenic plants accumulated new compounds, not present in either wild-type or vector-transformed plants. These were identified, by high-pressure liquid chromatography, as trans-resveratrol and trans-resveratrol-glucopyranoside. The amounts of trans-resveratrol and its piceid form were evaluated in the transgenic fruit. It was found that the content of the metabolite varied during fruit maturation to up to 53 microg/g fresh weight of total trans-resveratrol at the red stage of ripening. This metabolite accumulation was possibly dependent on a combination of sufficiently high levels of stilbene synthase and the availability of substrates. With the aim of verifing the metabolic impairment, the amounts of chlorogenic acid and naringenin in both transgenic and wild-type ripening fruit were compared and no dramatic variation in the synthesis profile of the two metabolites was noted. To our knowledge, no data are available on the assessment of the effects of the expression of the StSy gene on other antioxidant compounds present in tomato fruit. To establish whether the presence of a novel antioxidant molecule affected the redox regulation in transgenic tomato fruit cells, the effect of resveratrol accumulation on the naturally present antioxidant pool was analysed. We showed that, in transgenic fruit which accumulate trans-resveratrol, there is an increase in the levels of ascorbate and glutathione, the soluble antioxidants of primary metabolism, as well as in the total antioxidant activity. Conversely, the content of tocopherol and lycopene, which are membrane-located antioxidants, is not affected. Consistent with the increased antioxidant properties, the lipid peroxidation was lower in transformed than in wild-type fruit.

The potential of microarrays to assist shrimp breeding and production: a review

The shrimp aquaculture industry is a relatively new livestock industry, having developed over the past 30 years. Thus, it is poised to take advantage of new technologies from the outset of selective breeding programs. This contrasts with long established livestock industries, where there are already highly specialised breeds. This review focuses specifically on the potential application of microarrays to shrimp breeding. Potential applications of microarrays in selective breeding programs are summarised. Microarrays can be used as a rapid means to generate molecular markers for genetic linkage mapping, and genetic maps have been constructed for yeast, Arabidopsis and barley using microarray technology. Microarrays can also be used in the hunt for candidate genes affecting particular traits, leading to development of perfect markers for these traits (i.e. causative mutations). However, this requires that microarray analysis be combined with genetic linkage mapping, and that substantial genomic information is available for the species in question. A novel application of microarrays is to treat gene expression as a quantitative trait in itself and to combine this with linkage mapping to identify quantitative trait loci controlling the levels of gene expression; this approach may identify higher level regulatory genes in specific pathways. Finally, patterns of gene expression observed using microarrays may themselves be treated as phenotypic traits in selection programs (e.g. a particular pattern of gene expression might be indicative of a disease tolerant individual). Microarrays are now being developed for a number of shrimp species in laboratories around the world, primarily with a focus on identifying genes involved in the immune response. However, at present, there is no central repository of shrimp genomic information, which limits the rate at which shrimp genomic research can be progressed. The application of microarrays to shrimp breeding will be extremely limited until there is a shared repository of genomic information for shrimp, and the collective will and resources to develop comprehensive genomic tools for shrimp.

Genomics of berry fruits antioxidant components

Reactive oxygen and nitrogen metabolites, which are side products of cell metabolism, can produce a lot of damage in biological macromolecules and tissues, producing a number of chronic illnesses. On the other hand, antioxidant metabolites usually accumulated in fruits and vegetables can provide an effective protection by neutralizing these reactive molecules. Among comestible vegetables, berry fruits are considered one of the richest sources of antioxidant metabolites; hence, they represent a good model for molecular and biochemical investigations about the biosynthesis and the functional role of antioxidants in plants. This review illustrates how recent developments in the fields of genomics and bioinformatics can provide powerful tools to better understand the molecular mechanisms that trigger biosynthesis and accumulation of antioxidant metabolites in berries.

Evolution of flavors and scents

The world is filled with flavors and scents, which are the result of volatile compounds produced and emitted by plants. These specialized metabolites are the products of specific metabolic pathways. The terpenoid, fatty acid, and phenylpropanoid pathways contribute greatly to production of volatile compounds. Mechanisms that lead to evolution of volatile production in plants include gene duplication and divergence, convergent evolution, repeated evolution, and alteration of gene expression, caused by a number of factors, followed by change in enzyme specificity. Many examples of these processes are now available for three important gene families involved in production of volatile metabolites: the small molecule O-methyltransferases, the acyltransferases, and the terpene synthases. Examples of these processes in these gene families are found in roses, Clarkia breweri, and sweet basil, among others. Finally, evolution of volatile emission will be an exciting field of study for the foreseeable future.

An EST resource for cassava and other species of Euphorbiaceae

Cassava (Manihot esculenta) is a major food staple for nearly 600 million people in Africa, Asia, and Latin America. Major losses in yield result from biotic and abiotic stresses that include diseases such as Cassava Mosaic Disease (CMD) and Cassava Bacterial Blight (CBB), drought, and acid soils. Additional losses also occur from deterioration during the post-harvest storage of roots. To help cassava breeders overcome these obstacles, the scientific community has turned to modern genomics approaches to identify key genetic characteristics associated with resistance to these yield-limiting factors. One approach for developing a genomics program requires the development of ESTs (expressed sequence tags). To date, nearly 23,000 ESTs have been developed from various cassava tissues, and genotypes. Preliminary analysis indicates existing EST resources contain at least 6000-7000 unigenes. Data presented in this report indicate that the cassava ESTs will be a valuable resource for the study of genetic diversity, stress resistance, and growth and development, not only in cassava, but also other members of the Euphorbiaceae family.

A transcriptomics resource for wheat functional genomics

Grain development, germination and plant development under abiotic stresses are areas of biology that are of considerable interest to the cereal community. Within the Investigating Gene Function programme we have produced the resources required to investigate alterations in the transcriptome of hexaploid wheat during these developmental processes. We have single pass sequenced the cDNAs of between 700 and 1300 randomly picked clones from each of 35 cDNA libraries representing highly specific stages of grain and plant development. Annotated sequencing results have been stored in a publicly accessible, online database at http://www.cerealsdb.uk.net. Each of the tissue stages used has also been photographed in detail, resulting in a collection of high-quality micrograph images detailing wheat grain development. These images have been collated and annotated in order to produce a web site focused on wheat development (http://www.wheatbp.net/). We have also produced high-density microarrays of a publicly available wheat unigene set based on the 35 cDNA libraries and have completed a number of microarray experiments which validate their quality.

Gain and loss of fruit flavor compounds produced by wild and cultivated strawberry species

The blends of flavor compounds produced by fruits serve as biological perfumes used to attract living creatures, including humans. They include hundreds of metabolites and vary in their characteristic fruit flavor composition. The molecular mechanisms by which fruit flavor and aroma compounds are gained and lost during evolution and domestication are largely unknown. Here, we report on processes that may have been responsible for the evolution of diversity in strawberry (Fragaria spp) fruit flavor components. Whereas the terpenoid profile of cultivated strawberry species is dominated by the monoterpene linalool and the sesquiterpene nerolidol, fruit of wild strawberry species emit mainly olefinic monoterpenes and myrtenyl acetate, which are not found in the cultivated species. We used cDNA microarray analysis to identify the F. ananassa Nerolidol Synthase1 (FaNES1) gene in cultivated strawberry and showed that the recombinant FaNES1 enzyme produced in Escherichia coli cells is capable of generating both linalool and nerolidol when supplied with geranyl diphosphate (GPP) or farnesyl diphosphate (FPP), respectively. Characterization of additional genes that are very similar to FaNES1 from both the wild and cultivated strawberry species (FaNES2 and F. vesca NES1) showed that only FaNES1 is exclusively present and highly expressed in the fruit of cultivated (octaploid) varieties. It encodes a protein truncated at its N terminus. Green fluorescent protein localization experiments suggest that a change in subcellular localization led to the FaNES1 enzyme encountering both GPP and FPP, allowing it to produce linalool and nerolidol. Conversely, an insertional mutation affected the expression of a terpene synthase gene that differs from that in the cultivated species (termed F. ananassa Pinene Synthase). It encodes an enzyme capable of catalyzing the biosynthesis of the typical wild species monoterpenes, such as alpha-pinene and beta-myrcene, and caused the loss of these compounds in the cultivated strawberries. The loss of alpha-pinene also further influenced the fruit flavor profile because it was no longer available as a substrate for the production of the downstream compounds myrtenol and myrtenyl acetate. This phenomenon was demonstrated by cloning and characterizing a cytochrome P450 gene (Pinene Hydroxylase) that encodes the enzyme catalyzing the C10 hydroxylation of alpha-pinene to myrtenol. The findings shed light on the molecular evolutionary mechanisms resulting in different flavor profiles that are eventually selected for in domesticated species.

Comprehensive EST analysis of tomato and comparative genomics of fruit ripening

A large tomato expressed sequence tag (EST) dataset (152 635 total) was analyzed to gain insights into differential gene expression among diverse plant tissues representing a range of developmental programs and biological responses. These ESTs were clustered and assembled to a total of 31 012 unique gene sequences. To better understand tomato gene expression at a plant system level and to identify differentially expressed and tissue-specific genes, we developed and implemented a digital expression analysis protocol. By clustering genes according to their relative abundance in the various EST libraries, expression patterns of genes across various tissues were generated and genes with similar patterns were grouped. In addition, tissues themselves were clustered for relatedness based on relative gene expression as a means of validating the integrity of the EST data as representative of relative gene expression. Arabidopsis and grape EST collections were also characterized to facilitate cross-species comparisons where possible. Tomato fruit digital expression data was specifically compared with publicly available grape EST data to gain insight into molecular manifestation of ripening processes across diverse taxa and resulted in identification of common transcription factors not previously associated with ripening.

ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development

Gene expression profiling holds tremendous promise for dissecting the regulatory mechanisms and transcriptional networks that underlie biological processes. Here we provide details of approaches used by others and ourselves for gene expression profiling in plants with emphasis on cDNA microarrays and discussion of both experimental design and downstream analysis. We focus on methods and techniques emphasizing fabrication of cDNA microarrays, fluorescent labeling, cDNA hybridization, experimental design, and data processing. We include specific examples that demonstrate how this technology can be used to further our understanding of plant physiology and development (specifically fruit development and ripening) and for comparative genomics by comparing transcriptome activity in tomato and pepper fruit.