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First published online July 14, 2003; 10.1105/tpc.012963 American Society of Plant Biologists Activation Tagging in Tomato Identifies a Transcriptional Regulator of Anthocyanin Biosynthesis, Modification, and TransportExelixis Plant Sciences, Inc., Portland, Oregon 97224-7744 1 To whom correspondence should be addressed. E-mail hmathews{at}exelixis.com; fax 503-670-7703
We have developed a high-throughput T-DNA insertional mutagenesis program in tomato using activation tagging to identify genes that regulate metabolic pathways. One of the activation-tagged insertion lines (ant1) showed intense purple pigmentation from the very early stage of shoot formation in culture, reflecting activation of the biosynthetic pathway leading to anthocyanin accumulation. The purple coloration resulted from the overexpression of a gene that encodes a MYB transcription factor. Vegetative tissues of ant1 plants displayed intense purple color, and the fruit showed purple spotting on the epidermis and pericarp. The gene-to-trait relationship of ant1 was confirmed by the overexpression of ANT1 in transgenic tomato and in tobacco under the control of a constitutive promoter. Suppression subtractive hybridization and RNA hybridization analysis of the purple tomato plants indicated that the overexpression of ANT1 caused the upregulation of genes that encode proteins in both the early and later steps of anthocyanidin biosynthesis as well as genes involved in the glycosylation and transport of anthocyanins into the vacuole.
The genomes of higher plants are composed of thousands of genes that control growth, physiology, reproduction, and pathogen interaction traits. Understanding the functions of these genes is a major challenge, and a variety of forward- and reverse-genetics methods are being applied to this challenge. A classic genetics approach to understanding the functions of uncharacterized genes is to identify loss-of-function mutations in these genes and to screen for associated phenotypes. The limitations of classic mutagenesis strategies include the difficulty of identifying genes that (1) act redundantly, (2) are required during multiple stages of the life cycle, (3) result in early embryonic or gametophytic lethality, or (4) occur in species not suited for classic mutagenesis approaches. We have used "activation tagging" in tomato to facilitate the rapid functional analysis of genes involved in metabolic pathways. Activation tagging produces dominant mutations by means of the overexpression of endogenous genes with transcriptional enhancers that cause the ectopic expression of genes in the vicinity of the T-DNA insertion site (Borevitz et al., 2000
Tomato is a well-established model organism for the study of many biological processes. Tomato offers several features that enable studies on the development and ripening of fleshy fruit and on many plantpathogen interactions that affect economically important plants. Its moderately sized genome (950 Mb with hundreds of mapped traits and molecular markers), tolerance to inbreeding, amenability to genetic transformation, and diversity of secondary metabolism make tomato an excellent platform for genetic and molecular research (Tanksley, 1993
The tomato cultivar used in this study is Micro-Tom, a variety originally bred for home gardening purposes (Scott and Harbaugh, 1989
Generation of Activation-Tagged Lines of Micro-Tom Transgenic Lines Several types of Micro-Tom tissues, including leaf, stem, hypocotyl, and shoot tip, were tested for their ability to be transformed by Agrobacterium tumefaciens strain GV3101 containing pAG3202, a binary vector with four copies of 35S enhancers and a selection cassette containing nptII. Although all of the tissues tested gave transformed plants, the hypocotyl segments were the explant of choice because of the ease of manipulation and the consistently high rate of transformation (40 to 60%). Activation-tagged lines of Micro-Tom displayed variations from the wild-type untransformed plant in many phenotypic traits. From a population of 10,427 independent transgenic lines, 1338 transgenic lines (12.83%) exhibited variation from the wild type in one or more visually observable characteristics. The heritability of the observed variations was confirmed in a set of select mutants by evaluating T1 progeny (Table 1). The segregation ratio of the mutant phenotype in T1 indicated a dominant or semidominant trait. In addition to evaluating T1 progeny from plants observed to have a mutant phenotype in T0, we evaluated T1 progeny from 1014 randomly selected activation-tagged lines. Phenotypes not observed in the T0 generation were identified for 103 of these lines, indicating possible loss-of-function traits resulting from T-DNA integration. Ten percent of these lines produced T1 progeny with a visually observable variant phenotype (data not shown).
Some of the fruit mutants with varying color and shape are shown in Figure 1. The color phenotypes were of special interest in the present study as a means of finding genes involved in pigment biosynthesis. From among the various color mutants, an anthocyanin mutant (ant1) with prominent purple coloration was selected for complete characterization at the molecular, biochemical, and genetic levels. This anthocyanin mutant was identified at a very early stage of development in tissue culture as a purple-colored caulogenic callus of a hypocotyl explant. The T0 plant of the ant1 mutant had purplish leaves, stems and flowers with prominent purple striations, and fruit with purple cells on the epidermis, as shown in Figure 2.
The ANT1 Gene Encodes a MYB-Factor Protein The inheritance of the ant1 mutant followed a typical Mendelian pattern for a dominant trait controlled by a single gene. Of 18 seeds that were sown, 11 germinated; 3 were sensitive to kanamycin (indicating the absence of the transgene), and the surviving 8 kanamycin-resistant plants displayed anthocyanin accumulation (Table 1). The presence of a single T-DNA insertion in the anthocyanin mutant was confirmed by T-DNAspecific PCR and DNA gel blot hybridization (data not shown). As shown in Figure 3A, a single predicted gene was identified in the 6.4-kb rescued genomic fragment adjacent to the 35S enhancers. The predicted gene has three exons that result in an 825-nucleotide coding region and a 274amino acid protein. The translation start codon was 1810 bp away from the right T-DNA border. Reverse transcriptase (RT)PCR confirmed that the transcriptional expression of the predicted ANT1 transcript is upregulated in the activation-tagged mutant relative to the wild-type background (Figure 3B), and sequencing of the product confirmed the predicted gene structure. There are no ESTs in the public databases that exactly match the predicted coding sequence of ANT1, which, in combination with the low abundance of this transcript in wild-type tomato, indicates that the expression of this gene normally is low or restricted to specific tissues and developmental stages. The ANT1 gene is predicted to encode a MYB-factor protein. An amino acid sequence alignment of the predicted ANT1 protein with other plant transcription factors known to function in the regulation of the anthocyanin biosynthetic pathway is shown in Figure 4.
Recapitulation of the ant1 Mutant Phenotype To demonstrate a direct relationship between ANT1 overexpression and the pigmented phenotype, we transformed tomato cv Micro-Tom with the ANT1 genomic DNA expressed under a strong constitutive promoter, cassava vein mosaic promoter (Verdaguer et al., 1996
To determine whether the ANT1 gene product could function in other solanaceous plants, tobacco cv Wisconsin was transformed with the same ANT1 construct described above. Transgenic plants of tobacco expressing the ANT1 gene also gave a range of phenotypes, from green to slightly or intensely purple plants. Figure 7 shows an intensely purple tobacco plant expressing the tomato ANT1 gene. Of 89 independent transgenic events confirmed by genomic PCR, 56 had purple coloration in tobacco. RT-PCR analysis showed the expression of ANT1 transcript in all of the samples with purple color (Figure 7).
Quantitation of Anthocyanin Content and ANT1 Expression Levels in ANT1 Transgenic Tomato HPLC analysis with photodiode array detection was used to quantitate the anthocyanin content in three recapitulated ANT1 Micro-Tom lines designated BK, AW, and AX as well as in wild-type plants. All lines were grown in vitro and sampled in triplicate 3 weeks after seeds were sown. As shown in Figure 8, among the recapitulated lines, AX was by far the highest pigment accumulator, averaging 3574 µg of anthocyanin per gram fresh weight, an almost 500-fold increase over wild-type levels. BK had 294 µg/g fresh weight, and AW had 57 µg/g fresh weight. The amounts of anthocyanins detected in these lines correlated well with the levels of transcript expressed by these lines, as measured by RNA gel blot analysis (Figure 9). RNA gel blot analysis also showed the upregulation of a downstream gene that encodes glutathione S-transferase (GST) along with the increased expression of ANT1 (Figure 9C).
Further analysis of ant1 Micro-Tom leaf extracts by liquid chromatography/photodiode array tandem mass spectrometry indicated the presence of nine discrete anthocyanins. All had UV absorbance maxima near 520 nm, and their molecular weights in order of retention time were 773, 787, 801, 935, 949, 963, 919, 933, and 947. Fragmentation of the nine molecular ions yielded one of three daughter ions of molecular weight 303, 317, or 331, indicating the presence of delphinidin-, petunidin-, or malvidin-type anthocyanidins (aglycones), respectively. Comparison of the molecular weights and mass spectrometry fragmentation patterns of the tomato anthocyanins with common anthocyanin glycosylation and acylation motifs led us to conclude that ant1 Micro-Tom produces the 3-rutinoside-5-glucoside of delphinidin, petunidin, and malvidin. Further acylation of these pigments with p-coumaric acid or caffeic acid led to the production of six additional red to violet pigments (Table 2). All are known anthocyanins, and three have been reported previously in light-stressed tomatoes (Bovy et al., 2002
ANT1 Regulates a Variety of Genes Involved in Anthocyanin Accumulation Validation of gene expression via SMART cDNA gel blot hybridization is similar to RNA gel blot hybridization and can resolve the presence of different splice forms of differentially expressed transcripts. As shown in Figure 10, the overexpression of ANT1 resulted in the upregulation of genes that encode proteins in the early (chalcone synthase [CHS]) and late (dihydroflavonol reductase [DFR]) steps of anthocyanin biosynthesis. In addition, several other genes involved in anthocyanin molecule decoration and transportation were identified by suppression subtractive hybridization (SSH). A summary of the validated differentially expressed transcripts in the ANT1 transgenic tomato is presented in Table 3. The EST contig with the highest match to the SSH fragment was assigned a putative identity based on a BLASTX (Basic Local Alignment Search Tool) search against the nonredundant protein database in GenBank (Altschul et al., 1997 10 transmembrane helices required for the vacuolar transport of proanthocyanidins such as the Arabidopsis TT12 gene. The amino acid sequence alignment performed using the default parameters of CLUSTAL W showed the relative similarity of putative CHI and anthocyanin permease from tomato and other genera (Figures 11 and 12).
We have demonstrated the utility of an activation-tagging approach to induce genetic mutants in tomato using a high-throughput tissue culture transformation system. From a population of 10,427 T0 transgenic plants, 1338 showed visible phenotypic variations, and a subset of these tested in T1 confirmed the heritability of the observed traits (Table 1). In addition, analysis of the T1 plants from randomly selected activation-tagged lines gave novel variations in 103 of the 1014 lines analyzed in T1. These observed variation rates indicate the potential of activation-tagging technology as an effective mutagen in tomato. Based on recent estimates of the number, organization, and evolution of genes in the tomato genome (Van der Hoeven et al., 2002
Of the many observed pigmentation mutants, we have characterized one, ant1, in which the purple phenotype resulted from the overexpression of a predicted gene that encodes a MYB transcription factor. The gene was cloned and overexpressed in tomato and tobacco, demonstrating that the upregulation of ANT1 MYB factor was responsible for the observed color phenotype. The overexpression of this single transcription factor caused the heavy accumulation of purple color, whereas the simultaneous expression of two heterologous genes (transcription factors LC and C1 of maize) were necessary to produce high-flavonol tomatoes (Bovy et al., 2002
Characterization of anthocyanin mutants in a variety of plant species has led to the identification of genes that encode not only the enzymes of the anthocyanin biosynthetic pathways but also the regulatory elements that confer tissue-specific accumulation of anthocyanin (Dooner et al., 1991
ANT1 has a highly conserved R2R3 MYB domain from residues 11 to 116. When this region is aligned with the same region from other functionally characterized plant proteins involved in flavonoid accumulation, a high degree of conservation is evident (Figure 4A). The C termini among these proteins generally have little identity. Outside of the R2R3 domain, ANT1 displays amino acid sequence similarity only to AN2 (Figure 4B). The two sequences show 53% identity and 62% similarity over the length of the protein. Functional domains in these regulatory proteins have been identified. For example, the conserved Trp (or Ile) residues in the MYB repeats have been demonstrated to be involved in DNA binding (Li and Parish, 1995
SSH and SMART cDNA hybridization have revealed a suite of genes upregulated in plants overexpressing the ANT1 transcript. The ANT1 transgene itself was isolated by SSH as clone MT13, validating the experimental approach. The genes that encode proteins in the early and late biosynthetic pathways of anthocyanin synthesis, CHS and DFR, were upregulated in ANT1-overexpressing plants. DFR, a single-copy gene in tomato, is known to be represented by two transcript sizes resulting from alternating polyadenylation signals (Bongue-Bartelsman et al., 1994
The diverse group of transcriptional regulators controls not only anthocyanin biosynthesis but also their modification and transport into the vacuole. Overexpression of ANT1 upregulated genes likely encodes the decorating enzymes 3-O-glucosyltransferase and 5-O-glucosyltransferase as well as a type-I GST, a flavonoid binding protein required for vacuolar transport (similar to petunia AN9). Anthocyanins frequently are glycosylated, and glycosyltransferases are upregulated coordinately with other anthocyanin biosynthetic enzymes (Bovy et al., 2002
A gene with strong similarity to the petunia AN9 gene that encodes GST, which is required for efficient vacuolar sequestration (Mueller et al., 2000
Three new genes in tomato anthocyanin synthesis and accumulation were identified in ANT1 transgenic tomato by SSH: a gene similar to CHI (CHI-like), a HD-GL2 gene similar to Arabidopsis HD-GL2, and a putative permease similar to proteins with
The MTP96 transcript, which is upregulated in the ANT1 transgenic line, encodes a protein with similarity to CHI. The CHI-like gene product encoded by MTP96 is most similar to the Arabidopsis At3g63170 gene product and is only 17% identical (32% similar) to the petunia CHI-A gene product (Figure 12). However, the MTP96 product lacks the conserved residues reported to be involved in (2S)-naringenin binding and substrate preference determination (Jez et al., 2000
Finally, the MTP77 clone that encodes a putative anthocyanin permease was characterized. The complete MTP77 cDNA sequence was assembled, translated, and compared with the Arabidopsis TT12 gene product and two other related Arabidopsis gene products (Figure 12). The MTP77 cDNA encodes a protein that is 36% identical (56% similar) to TT12 but is even more like At4g00350 (53% identical and 68% similar) and At4g25640 (61% identical and 71% similar). TT12 resembles multidrug secondary transporters in the MATE family and is likely to mediate the vacuolar sequestration of proanthocyanidins in the seed coat of Arabidopsis (Debeaujon et al., 2001
Mutant analysis in Arabidopsis also has led to the identification of genes involved in the cell typespecific accumulation of anthocyanins (ANL2; Kubo et al., 1999
Genetic mutants have always played a central role as tools for research into the developmental processes of plants. A number of genes have been isolated in tomato by insertional mutagenesis using targeted tagging of Ac/Ds elements (Jones et al., 1994
Activation-Tagging Construct The activation-tagging construct pSKI015 (Weigel et al., 2000
Plant Transformation
Agrobacterium strain GV3101 containing the binary vector plasmid mentioned above was streaked on MGL medium (5 mg/L tryptone, 2.5 mg/L yeast extract, 5 mg/L NaCl, 5 mg/L mannitol, 1.17 mg/L sodium glutamate, 0.33 mg/L K2HPO4·3H2O, 0.1 mg/L MgSO4, and 0.02 mg/L biotin at pH 5.4) with 100 mg/L carbenicillin and grown at 28°C for 2 to 3 days. A single colony was picked from the plate and grown in 30 to 40 mL of MGL medium with 50 µM acetosyringone and 50 mg/L carbenicillin overnight. The bacteria were centrifuged at 4500 relative centrifugal force for 15 min to remove antibiotics and then suspended in MGL or liquid plant cocultivation medium (MS salts, Linsmaier and Skoog [1965]
Hypocotyls and stems were segmented into 3- to 5-mm sections. Leaves were cut into 4-mm cross-sections exclusive of the shoot tip and petiole. Shoot tips were excised from the seedlings, leaving 2 to 3 mm of hypocotyl for ease of handling. Cotyledons were removed and the shoot tips were cut in half longitudinally, being careful to bisect the meristem. The explants were immersed in Agrobacterium suspension for 15 min, blotted onto sterile filter paper, and plated on cocultivation medium (MS salts, Linsmaier and Skoog [1965]
Greenhouse Evaluation of Activation-Tagged Micro-Tom Transgenic Plants Morphological observations were made throughout the development of the T0 plants for phenotypes such as plant stature; growth habit; leaf size, shape, texture, and color; flower size, shape, and color; fruit size, shape, and color; and seed set. Digital images were captured for plants with interesting morphological phenotypic modifications. Fruit was collected at maturity and allowed to ferment in a plastic bag before seed collection. The collected seeds were dried and cataloged in a temperature- and humidity-controlled chamber for future use. Leaf and fruit tissues were frozen in liquid nitrogen and stored at -80°C for biochemical and molecular analyses. T1-generation plants were grown to evaluate genetic segregation, confirm the mutant phenotypes observed in the T0 generation, and screen for possible loss-of-function mutations. The emerging seedlings were sprayed with kanamycin at 1.0 mg/L three times at 2-day intervals to identify plants that were nulls without the transgene. Approximately 1 week after the last spraying, the lines were scored for germination rate as well as seedling resistance to kanamycin. The kanamycin-resistant seedlings were given individual identifier codes and transplanted to 4-inch pots for further observations like those used for T0 transplants.
Plasmid Rescue of DNA Flanking the T-DNA in the ant1 Mutant
Reverse TranscriptasePCR
Recapitulation of the ant1 Phenotype in Tomato and Tobacco
RNA Gel Blot Hybridization DNA fragments used as probes were amplified by PCR from tomato SMART cDNA using oligonucleotide primers designed for DFR (DFR-F, 5'-GCTTGTCATGAGACTCCTTGAACG-3'; DFR-R, 5'-CGCACCATCTTAGCCACATCG-3') and for ANT1 (ANT1-F, 5'-GGATCCTATATTATCAAATTATTATGAACA-3'; ANT1-R, 5'-ACTAGTACATATCTTTTAATCAAGTAGATT-3'). The probes used to validate the differentially ex-pressed transcript were amplified by PCR from the pCR2.1 vector with oligonucleotide primers complementary to the vector flanking the TA cloning site (M13F, 5'-CGCCAGGGTTTTCCCAGTCACGAC-3'; M13R, 5'-AGCGGATAACAATTTCACACAGGA-3'). Amplification of all probe fragments was performed for 30 cycles in a Perkin-Elmer 480 thermal cycler using a 60°C annealing temperature and a 1-min extension.
The amplified probe fragments (
Suppression Subtractive Hybridization
SMART cDNA was digested with RsaI, and adaptors were ligated according to the protocol supplied with the Clontech PCR-Select cDNA Subtraction Kit (K1804). Two rounds of subtractive hybridization were performed with the wild-type and ANT1 transgenic SMART cDNA samples, including both forward (MTP) and reverse (MTC) subtractions. Primary and secondary PCR amplifications were performed using 27 and 12 cycles, respectively. The resulting pools of differentially expressed fragments were cloned into a TA cloning kit (pCR2.1; Invitrogen, Carlsbad, CA). The ligation reactions were purified over a G-50 column before transformation into INV To estimate the relative transcript abundance in each pool of cloned fragments, 48 colonies per transformation were chosen for PCR colony screening with primers flanking the TA cloning site (M13F and M13R as described above). The 96 reaction products (amplified insert) were separated on duplicate agarose gels, transferred to nylon membranes with 0.4 M NaOH, and probed separately with SMART cDNA from either wild-type or ANT1 transgenic Micro-Tom. Probe labeling, hybridization, and signal detection were performed as described previously. The average signal intensity of the 48 cloned fragments from the forward subtraction (MTP) was twofold greater than that from the reverse subtraction (MTC), indicating that the MTP pool was enriched in upregulated transcript fragments (data not shown). The clones showing the highest fold change in expression between the wild-type and transgenic samples were selected for validation by DNA gel blot hybridization and for DNA sequencing. Plasmid DNA templates were sequenced using the M13F and M13R primers on an ABI3100 DNA sequencer. Vector, primer, and poly(A) sequences were removed from the output before Basic Local Alignment Search Tool (BLASTN) analysis against the tomato EST collection in GenBank, assembled into the least number of contigs. For DNA gel blot hybridization, SMART cDNA (3 µg/lane) was separated, transferred to nylon membranes (0.4 M NaOH), and hybridized with labeled PCR fragments corresponding to candidate regulated transcript fragments. Hybridization with probes to ANT1, DFR, and GST verified that these genes were upregulated in the ANT1 transgenic plants. The results also confirmed that the SMART cDNA gel blot results were similar to results from RNA gel blot hybridization, even including the ability to resolve different splice and polyadenylated forms of the GST and DFR transcripts. The 5' and 3' ends of the MTP77 cDNA were amplified from SMART cDNA using nested sequence-specific primers and primers complementary to the adaptors on the ends of the SMART cDNA fragments. Reactions were set up according to the protocol supplied with the Universal GenomeWalker Kit (Clontech, K1807-1) and the Advantage Genomic Polymerase Mix (Clontech) using a Perkin-Elmer 480 thermal cycler. Primary amplifications consisted of 7 cycles (94°C for 25 s and 70°C for 3 min), 32 cycles (94°C for 25 s and 65°C for 3 min), and 1 cycle (67°C for 7 min). Secondary amplifications consisted of 5 cycles (94°C for 25 s and 68°C for 3 min), 20 cycles (94°C for 25 s and 63°C for 3 min), and 1 cycle (67°C for 7 min). The 5' end of the MTP77 cDNA was amplified in the first round with SMART PCRIIA (5'-AAGCAGTGGTATCAACGCAGAGT-3') and MTP77_F1 (5'-GAAAGACACAAGTAGCTAGCAGGATTA-3') and in the second round with PCRIIA-UP (5'-GTGGTATCAACGCAGAGTACGCGG-3') and MTP77_F2 (5'-CCATATGCCTGGCCACATAGTGTCTC-3'). The 3' end of MTP77 cDNA was amplified in the first round with SMART PCRIIA and MTP77_R1 (5'-CTTCAAGCTCAGAGTAAAGTGGATGT-3') and in the second round with PCRIIA-DOWN (5'-GTGGTATCAACGCAGAGTACTTTTT-3') and MTP77_R2 (5'-GGCTCTTTATATATACACTTGAATGGGG-3'). A full-length MTP77 cDNA clone then was amplified from SMART cDNA using sequence-specific primers based on the sequences of the 3' and 5' ends. The 1.7-kb fragment was cloned and sequenced.
Biochemical Analysis
HPLC Conditions
Quantitation
Liquid Chromatography/Tandem Mass Spectrometry Upon request, materials integral to the findings presented in this publication will be made available in a timely manner to all investigators on similar terms for noncommercial research purposes. To obtain materials, please contact D. Ry Wagner, rwagner{at}exelixis.com.
Accession Numbers
Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.012963. Received April 15, 2003; accepted June 9, 2003.
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