Abstract

3-Deoxyanthocyanidins are the unique phytoalexins synthesized by sorghum in response to fungal inoculation. They are structurally related to anthocyanins but the final steps of their pathogen-inducible biosynthesis are not fully understood. We have identified new flavonoid structural genes from the recently completed sorghum BTx623 genome sequence. The biochemical functions of the different expressed sorghum genes were established in planta by complementation in the appropriate Arabidopsis transparent testa mutants. There is a family of nine chalcone synthase genes which are all inducible by fungal inoculation in sorghum seedlings. Specific dihydroflavonol 4-reductase (DFR) genes responsive to conditions which stimulated anthocyanin accumulation (SbDFR1) or 3-deoxyanthocyanidin production (SbDFR3) were identified. Recombinant SbDFR1 and SbDFR3 were found to function as typical DFRs by accepting dihydroflavonol substrates. On the other hand, both DFRs showed substantially lower but detectable NADPH-dependent activities toward flavanones. Reduction of flavanones to flavan-4-ols is a reaction step required for 3-deoxyanthocyanidin production. Flavanone 3-hydroxylase (F3H) converts flavanones to dihydroflavonols for anthocyanin biosynthesis. In sorghum seedlings, expression of two F3H genes was either absent or strongly suppressed during the accumulation of 3-deoxyanthocyanidins. Under such conditions, most flavanones are expected to be reduced by the pathogen-induced SbDFR3 for the formation of flavan-4-ols. Our work also revealed that 3-deoxyanthocyanidin accumulation and SbDFR3 expression were induced by methyl jasmonate treatment in sorghum roots but the stimulation effects were antagonized by salicylic acid.

Introduction

3-Deoxyanthocyanins (orange-red coloration) are structurally similar to anthocyanins except for the absence of C-3 hydroxylation. They are the major pigments in sinningia (Sinningia cardinalis) flowers (Winefield et al. 2005) and are found in silk tissues of certain maize lines (Halbwirth et al. 2003). Sorghum (Sorghum bicolor L.) is considered to be the only dietary source for 3-deoxyanthocyanins which are present in large quantities up to 10 mg g−1 in the bran of some cultivars (Awika et al. 2004). Many plants use the products of secondary metabolism to protect themselves from pathogens. In sorghum, this response is an active process which results in rapid accumulation of high levels of 3-deoxyanthocyanidin phytoalexins in infected tissues (Snyder and Nicholson 1990). We identified these compounds as luteolinidin, apigeninidin and their methoxylated derivatives, which are all present as aglycones (Lo et al. 1996, Wharton et al. 2000). In leaves, these phytoalexins first appear in the cells under fungal attack, where they accumulate in cytoplasmic inclusion bodies (Snyder and Nicholson 1990). The inclusions migrate to the site of attempted penetration, become pigmented and ultimately release their contents, killing both the plant cell and the fungus. We also demonstrated that the 3-deoxyanthocyanidin phytoalexins represent a significant component of resistance against the fungal pathogen Colletotrichum sublineolum (Lo et al. 1999), the causal agent of anthracnose which is a major disease affecting the worldwide production of sorghum.

Flavonoids as dietary constituents are increasingly popular because of their health beneficial properties as antioxidant and anticancer agents. Anthocyanins from different sources have been shown to suppress cancer cell proliferation and induce apotosis (Yi et al. 2005, Zhang et al. 2005). We and other laboratories have recently reported that the 3-deoxyanthocyanins have strong antiproliferative activities against several human cancer cell lines (Shih et al. 2007, Yang et al. 2009). In fact, they were shown to be more cytotoxic than their anthocyanidin analogs (Shih et al. 2007). In addition, sorghum extracts rich in 3-deoxyanthocyanins were demonstrated to induce phase II enzymes (Yang et al. 2009), which is considered as an indicator of protection against carcinogens in animal cells (Gao et al. 2006). Moreover, the 3-deoxyanthocyanidins show higher color stability to pH, temperature and light changes than the anthocyanidins and their glycosides (Awika et al. 2004). They have absorption maxima lower than 480 nm, allowing them to be used as a potential replacement of artificial yellow and orange pigments (Awika et al. 2004). Thus, the 3-deoxyanthocyanidins also represent a new source of natural colorants with nutraceutical values.

The health benefits of 3-deoxyanthocyanidins to both plants and humans highlight the importance of elucidating their route of biosynthesis. Flavonoid biosynthesis begins with a condensation reaction catalyzed by chalcone synthase (CHS) converting phenylpropanoid-CoA and malonyl-CoA into chalcones, followed by isomerization into flavanones by chalcone isomerase (CHI). It is from naringenin that the anthocyanidin and 3-deoxyanthocyanidin pathways are believed to diverge from each other (Fig. 1). In the anthocyanidin pathway, flavanone-3-hydroxylase (F3H) catalyzes the C-3 hydroxylation of flavanones, followed by an NADPH-dependent reduction of the C-4 carbonyl group by dihydroflavonol 4-reductase (DFR). Removal of the resulting hydroxyl group then occurs via the anthocyanidin synthase (ANS)-catalyzed reaction. In sorghum, it has been demonstrated that fungal inoculation resulted in de novo synthesis of 3-deoxyanthocyanidins. Thus, infected seedlings incorporated [14C]phenylalanine into 3-deoxyanthocyanidins within 48 h post-inoculation (Wharton and Nicholson 2000). Activities of the key branch-point enzymes phenylalanine ammonia-lyase and CHS and their gene expression were induced within 6 h of fungal inoculation (Hipskind et al. 1996). However, the molecular components responsible for the final steps in the pathogen-inducible 3-deoxyanthocyanidin pathway in sorghum remain unidentified. DFR-type reduction and ANS-type dehydrogenation/dehydroxylation reactions similar to those in the anthocyanidin pathway have been proposed for the synthesis of 3-deoxyanthocyanidins, presumably without the involvement of F3H (Fig. 1). In Northern hybridization experiments using maize DFR and ANS cDNAs as probes, Hipskind et al. (1996) demonstrated that the homologous genes in sorghum were not expressed during the pathogen- inducible accumulation of 3-deoxyanthocyanidins, leading to their conclusion that 3-deoxyanthocyanidin biosynthesis does not occur via a pathway similar to that for the normal anthocyanins.

Fig. 1

Biosynthesis pathway of anthocyanidins and 3-anthocyanidins in sorghum. CHS is the committed enzyme for flavonoid biosynthesis. Flavanones, which are isomerized by CHI from chalcones, are the common substrates for the formation of different classes of flavonoids, including anthocyanidins and 3-deoxyanthocyanidins. The sequential activities of F3H, DFR and ANS convert flavanones to anthocyanidins. A pathogen-inducible DFR gene (SbDFR3) described in the present study is involved in the reduction of flavanones to flavan-4-ols. The final step leading to 3-deoxyanthocyanin formation remains uncharacterized. Arabidopsis tt mutations in the different enzymatic steps are indicated.

Fig. 1

Biosynthesis pathway of anthocyanidins and 3-anthocyanidins in sorghum. CHS is the committed enzyme for flavonoid biosynthesis. Flavanones, which are isomerized by CHI from chalcones, are the common substrates for the formation of different classes of flavonoids, including anthocyanidins and 3-deoxyanthocyanidins. The sequential activities of F3H, DFR and ANS convert flavanones to anthocyanidins. A pathogen-inducible DFR gene (SbDFR3) described in the present study is involved in the reduction of flavanones to flavan-4-ols. The final step leading to 3-deoxyanthocyanin formation remains uncharacterized. Arabidopsis tt mutations in the different enzymatic steps are indicated.

In this study, we attempted to characterize a collection of key flavonoid structural genes (CHS, CHI, F3H, DFR and ANS) which were retrieved by bioinformatics searches against the sorghum (cultivar BTx623) genome sequence. To establish their in planta biochemical functions, the sorghum genes were transformed to Arabidopsis transparent testa (tt) mutants defective in the corresponding enzymatic steps for complementation analysis. Their gene expression was investigated in sorghum seedlings following fungal inoculation or illumination. We have identified specific CHS- and DFR-encoding genes which are up-regulated during the pathogen-induced 3-deoxyanthocyanidin accumulation. Recombinant enzyme assays demonstrated that both the light-inducible and pathogen-inducible DFR proteins were able to convert flavanones to flavan-4-ols, which are the immediate precursors for 3-deoxyanthocyanidins. On the other hand, the expression of anthocyanidin structural genes was found to be strongly suppressed during 3-deoxyanthocyanidin biosynthesis. Our work also revealed that 3-deoxyanthocyanidin accumulation can be induced in sorghum roots by methyl jasmonate (MeJA) but its stimulation effect is antagonized by salicylic acid (SA) treatment.

Results

Genome organization of flavonoid structural genes in sorghum

Previously, we isolated seven CHS genes (SbCHS1–SbCHS7) from a sorghum genomic bacterial artificial chromosome (BAC) library derived from BTx623 (Lo et al. 2002), the same cultivar which was used for the genome sequencing project (Paterson et al. 2008). The sorghum CHS genes are highly conserved, including the coding and untranslated regions. They all have a single intron and their encoded proteins share at least 97.5% amino acid sequence identity (Lo et al. 2002). Analysis of the recently completed BTx623 genome sequence data annotated at Phytozome v4.0 (http://www.phytozome.net/index.php) revealed that all these genes are located on chromosome 5 within a region of approximately 152 kb (Table 1). In particular, three tandem copies of SbCHS2 (SbCHS2a, SbCHS2b and SbCHS2c) were found in a 22 kb region. They are completely identical in their putative promoter (>2 kb upstream of the initiation codon), coding region, intron and the 5′- and 3′-untranslated regions. On the other hand, two sorghum genes (A1-a and A1-b) homologous to the maize DFR-encoding gene A1 were identified by previous comparative mapping analyses of the sorghum and maize genomes (Chen et al. 1997, Chen et al. 1998). In the BTx623 genome, we found that A1-a (SbDFR1) and A1-b (SbDFR2) are located on chromosome 3 (Table 1) and both genes contain three introns. Further bioinformatics searches retrieved two additional DFR genes which are located on different chromosomes: SbDFR3 (no introns) on chromosome 4 and SbDFR4 (three introns) on chromosome 9.

Table 1

Genome analysis of flavonoid structural genes in sorghum (BTx623)

Gene name Position Gene identifier mRNA (NCBI) 
Chalcone synthase    
SbCHS5 Chr 5: 49347424. .49351196 (+) Sb05g020150.1 XM_002449571 
SbCHS4 Chr 5: 49368387. .49370616 (−) Sb05g020160.1 XM_002450825 
SbCHS2a Chr 5: 49381777. .49383147 (−) Sb05g020170.1 XM_002450826 
SbCHS2b Chr 5: 49392232. .49393602 (−) Sb05g020180.1 XM_002450827 
SbCHS2c Chr 5: 49402563. .49404240 (−) Sb05g020190.1 XM_002450828 
SbCHS1 Chr 5: 49414226. .49416106 (−) Sb05g020200.1 XM_002450874 
SbCHS3 Chr 5: 49430465. .49432213 (−) Sb05g020210.1 XM_002450830 
SbCHS7 Chr 5: 49473660. .49475306 (−) Sb05g020220.1 XM_002450831 
SbCHS6 Chr 5: 49496992. .49500070 (−) Sb05g020230.1 XM_002450832 
Chalcone isomerase    
SbCHI Chr 1: 2669008. .2670703 (+) Sb01g003330.1 XM_002463631 
Flavanone 3-hydroxylase    
SbF3H1 Chr 6: 60106108. .60107732 (−) Sb06g031790.1 XM_002448658 
SbF3H2 Chr 6: 60109782. .60111313 (−) Not assigned GU320740 
Dihydroflavonol 4-reductase    
SbDFR1 (A1-aChr 3: 57039148. .57040668 (+) Sb03g028880.1 XM_002455970 
SbDFR2 (A1-bChr 3: 57050278. .57051815 (+) Sb03g028890.1 XM_002455971 
SbDFR3 Chr 4: 4074924. .4076251 (+) Sb04g004290.1 XM_002451541 
SbDFR4 Chr 9: 4191437. .4193565 (−) Sb09g003710.1 XM_002440548 
Anthocyanidin synthase    
SbANS Chr 4: 83230. .84739 (+) Sb04g000260.1 XM_002451291 
Gene name Position Gene identifier mRNA (NCBI) 
Chalcone synthase    
SbCHS5 Chr 5: 49347424. .49351196 (+) Sb05g020150.1 XM_002449571 
SbCHS4 Chr 5: 49368387. .49370616 (−) Sb05g020160.1 XM_002450825 
SbCHS2a Chr 5: 49381777. .49383147 (−) Sb05g020170.1 XM_002450826 
SbCHS2b Chr 5: 49392232. .49393602 (−) Sb05g020180.1 XM_002450827 
SbCHS2c Chr 5: 49402563. .49404240 (−) Sb05g020190.1 XM_002450828 
SbCHS1 Chr 5: 49414226. .49416106 (−) Sb05g020200.1 XM_002450874 
SbCHS3 Chr 5: 49430465. .49432213 (−) Sb05g020210.1 XM_002450830 
SbCHS7 Chr 5: 49473660. .49475306 (−) Sb05g020220.1 XM_002450831 
SbCHS6 Chr 5: 49496992. .49500070 (−) Sb05g020230.1 XM_002450832 
Chalcone isomerase    
SbCHI Chr 1: 2669008. .2670703 (+) Sb01g003330.1 XM_002463631 
Flavanone 3-hydroxylase    
SbF3H1 Chr 6: 60106108. .60107732 (−) Sb06g031790.1 XM_002448658 
SbF3H2 Chr 6: 60109782. .60111313 (−) Not assigned GU320740 
Dihydroflavonol 4-reductase    
SbDFR1 (A1-aChr 3: 57039148. .57040668 (+) Sb03g028880.1 XM_002455970 
SbDFR2 (A1-bChr 3: 57050278. .57051815 (+) Sb03g028890.1 XM_002455971 
SbDFR3 Chr 4: 4074924. .4076251 (+) Sb04g004290.1 XM_002451541 
SbDFR4 Chr 9: 4191437. .4193565 (−) Sb09g003710.1 XM_002440548 
Anthocyanidin synthase    
SbANS Chr 4: 83230. .84739 (+) Sb04g000260.1 XM_002451291 

Sorghum genes encoding CHI, F3H and ANS have not been reported in the literature previously. Using the corresponding maize sequences, we were able to identify the homologous sequences from the BTx623 genome. For example, two genes located on chromosome 6 were found to encode F3H-like proteins (Table 1). Both SbF3H1 and SbF3H2 show around 90% sequence identity to maize F3H (NCBI accession No. AAA91227). However, SbF3H2 was not annotated as a gene locus in the Phytozome v4.0 database. We determined the coding sequence through the isolation of a full-length cDNA by reverse transcription–PCR (RT–PCR; data not shown). On the other hand, both CHI and ANS appear to be encoded by single genes: SbCHI (three introns) on chromosome 1 and SbANS (no introns) on chromosome 4, and their encoded proteins are 91 and 82% identical to maize CHI (NCBI accession No. Q08704) and A2 (ANS) (NCBI accession No, CAA39022), respectively.

Expression of flavonoid structural genes in sorghum seedlings

The de novo biosynthesis of 3-deoxyanthocyanidin phytoalexins in sorghum is a light-independent response to attempted pathogen infection (Weiergang et al. 1996). In this study, RT–PCR analysis was first performed to examine the expression of the different flavonoid structural genes described above in inoculated sorghum seedlings kept in darkness or in light-grown non-infected seedlings (Fig. 2). The availability of the complete genome sequence data has allowed the design of gene-specific primers derived from the 3′-untranslated regions for the different families of flavonoid structural genes in sorghum. The maize fungal pathogen Cochliobolus heterostrophus, which is known to cause rapid and intense phytoalexin accumulation in sorghum mesocotyls (Hipskind et al. 1996), was used for the inoculation experiments. Following light exposure, anthocyanin pigments accumulate in the mesocotyl tissues of some sorghum cultivars, e.g. DK 46 (Lo and Nicholson 1998), but not in BTx623 (Lo et al. 1999). Pigmentation phenotypes of the different sorghum cultivars used in this study are shown in Table 2.

Fig. 2

Semi-quantitative RT–PCR (28 cycles) expression analysis of flavonoid structural genes in sorghum seedlings. Four-day-old etiolated seedlings were used for the experiments. RNA samples were prepared from mesocotyl tissues collected at the indicated time points (hours) following illumination or inoculation (C. heterostrophus). BTx623 seedlings produce the pathogen-induced 3-deoxyanthocyanidins but do not synthesize the light-induced anthocyanin pigments. DK46 is a pigmented cultivar which accumulates anthocyanin in mesocotyls after light exposure. Actin expression was used as the internal control. L, light exposure; D, dark incubation; D/I, dark incubation and inoculation.

Fig. 2

Semi-quantitative RT–PCR (28 cycles) expression analysis of flavonoid structural genes in sorghum seedlings. Four-day-old etiolated seedlings were used for the experiments. RNA samples were prepared from mesocotyl tissues collected at the indicated time points (hours) following illumination or inoculation (C. heterostrophus). BTx623 seedlings produce the pathogen-induced 3-deoxyanthocyanidins but do not synthesize the light-induced anthocyanin pigments. DK46 is a pigmented cultivar which accumulates anthocyanin in mesocotyls after light exposure. Actin expression was used as the internal control. L, light exposure; D, dark incubation; D/I, dark incubation and inoculation.

Table 2

Pigmentations in seedlings of the different sorghum cultivars analyzed in this study

Treatment BTx623 DK46 DK18 
Light None Anthocyanina None 
Dark None None None 
Inoculation (light) 3-Deoxyanthocyanidinsa Anthocyanina (reduced) + 3-deoxyanthocyanidinsa 3-Deoxyanthocyanidinsa 
Inoculation (dark) 3-Deoxyanthocyanidinsa 3-Deoxyanthocyanidinsa 3-Deoxyanthocyanidinsa 
MeJA root treatment None None 3-Deoxyanthocyanidinsb 
Treatment BTx623 DK46 DK18 
Light None Anthocyanina None 
Dark None None None 
Inoculation (light) 3-Deoxyanthocyanidinsa Anthocyanina (reduced) + 3-deoxyanthocyanidinsa 3-Deoxyanthocyanidinsa 
Inoculation (dark) 3-Deoxyanthocyanidinsa 3-Deoxyanthocyanidinsa 3-Deoxyanthocyanidinsa 
MeJA root treatment None None 3-Deoxyanthocyanidinsb 

All seedlings were planted in the dark to allow elongation of mesocotyls before light and inoculation treatments.

a Detected in mesocotyls.

b Detected in roots.

As shown in Fig. 2A, induced expression of all the CHS genes was detected in BTx623 mesocotyl tissues after the fungal inoculation. On the other hand, light-up-regulated expression was only detected for SbCHS5 which is expressed at slightly lower levels in the dark. Similar to SbCHS5, expression of the single-copy gene SbCHI was induced by either light or pathogen inoculation in the BTx623 seedlings. When the genes encoding the different downstream flavonoid enzymes (F3H, DFR and ANS) were examined, none of them was found to be expressed in the illuminated BTx623 seedlings (Fig. 2B), consistent with the absence of light-induced anthocyanin accumulation in the mesocotyls. In contrast, SbDFR3 expression was strongly induced in the inoculated BTx623 seedlings. On the other hand, expression of SbF3H1, SbF3H2, SbDFR1 and SbANS was activated in the pigmented mesocotyls of DK46 seedlings following illumination (Fig. 2B). However, SbDFR2 and SbDFR4 expression was not detectable in the seedlings of either sorghum cultivar under our experimental conditions (data not shown). Previously, we have demonstrated that the light- induced anthocyanin pigmentation in sorghum mesocotyls was reduced by fungal inoculation (Lo and Nicholson 1998). Here, we further examined the expression of the individual F3H-, DFR- and ANS-encoding genes in DK46 seedlings which were exposed to both stimuli of light and fungal inoculation simultaneously. Using real-time quantitative RT–PCR analysis, the light-inducible expression of SbF3H1, SbF3H2, SbDFR1 and SbANS was found to be suppressed substantially (>80%) after fungal inoculation (Fig. 3). In contrast, the pathogen-inducible SbDFR3 expression was not affected in the light-grown inoculated DK46 seedlings which produced the 3-deoxyanthocyanidin phytoalexins. Expression of SbDFR2 and SbDFR4 was not detected (data not shown).

Fig. 3

Real-time RT–PCR analysis of relative expression levels of sorghum genes encoding the flavonoid downstream enzymes (F3H, DFR and ANS) in inoculated DK46 seedlings placed under light. Mesocotyl tissues were collected for RNA extraction after 24 h of illumination/inoculation.

Fig. 3

Real-time RT–PCR analysis of relative expression levels of sorghum genes encoding the flavonoid downstream enzymes (F3H, DFR and ANS) in inoculated DK46 seedlings placed under light. Mesocotyl tissues were collected for RNA extraction after 24 h of illumination/inoculation.

Induction of 3-deoxyanthocyanidin production and SbDFR3 expression in sorghum roots by MeJA

During our investigations on the effects of different plant signaling compounds on defense gene expression, we observed the appearance of orange pigmentation in roots of the sorghum cultivar DK18 seedlings within 24 h of MeJA treatment (Fig. 4A). Methanol extractions were then performed on the root tissues for metabolite analysis. As shown in Fig. 4B, the accumulation of apigeninidin in the MeJA-treated roots was confirmed by tandem mass spectrometry (MS/MS) analysis. Interestingly, the MeJA-induced 3-deoxyanthocyanidin accumulation was suppressed by co-treatment with SA (Fig. 4A). The expression levels of the genes encoding the flavonoid downstream enzymes (F3H, DFR and ANS) were then examined in seedling roots following the different chemical treatments. RT–PCR experiments revealed the induction of SbDFR3 expression in the MeJA-treated, pigmented roots (Fig. 4C). In contrast, expression of SbF3H1, SbF3H2, SbDFR1, SbDFR2, SbDFR4 and SbANS was not activated under the same conditions (data not shown). On the other hand, SbDFR3 expression was not detectable in roots which were treated with both MeJA and SA (Fig. 4C), consistent with the SA suppression of MeJA-induced 3-deoxyanthocyanidin accumulation (Fig. 4A).

Fig. 4

MeJA induction of 3-deoxyanthocyanidin accumulation in sorghum roots. (A) Sorghum cultivar DK18 seedlings were treated with the indicated chemicals. Note the orange pigmentation in the MeJA-treated root and the repression of pigmentation in the JA/MeJA-treated root. (B) Metabolite analysis of MeJA-treated root extracts confirmed the accumulation of apigeninidin. The MS/MS spectrum shown is identical to that obtained for an authentic standard (not shown). (C) RT–PCR (28 cycles) analysis of SbDFR3 expression in sorghum roots following the different chemical treatments. Actin expression was used as the internal control.

Fig. 4

MeJA induction of 3-deoxyanthocyanidin accumulation in sorghum roots. (A) Sorghum cultivar DK18 seedlings were treated with the indicated chemicals. Note the orange pigmentation in the MeJA-treated root and the repression of pigmentation in the JA/MeJA-treated root. (B) Metabolite analysis of MeJA-treated root extracts confirmed the accumulation of apigeninidin. The MS/MS spectrum shown is identical to that obtained for an authentic standard (not shown). (C) RT–PCR (28 cycles) analysis of SbDFR3 expression in sorghum roots following the different chemical treatments. Actin expression was used as the internal control.

Complementation of Arabidopsis flavonoid mutants by the sorghum flavonoid genes

The Arabidopsis tt mutants are deficient in different flavonoid enzyme activities (Fig. 1), resulting in the lack of flavonoid accumulation in different tissues. The in planta biochemical function of SbCHS2 was previously established by complementation analysis in transgenic tt4 mutants (Yu et al. 2005). Due to their high degree of sequence identity (>97.5%), all the other SbCHS genes are also expected to encode functional CHS enzymes. In this study, the coding regions of the other flavonoid structural genes which showed expression following illumination or fungal inoculation (Fig. 2) were placed under the control of the 35S promoter and transformed into the appropriate Arabidopsis tt mutants. Transgene expression was confirmed by RT–PCR in 14-day-old T1 seedlings (data not shown) and three independent lines for each transgene were selected for phenotypic investigations. Low nitrogen is a stress condition known to induce the anthocyanin biosynthesis pathway in Arabidopsis wild-type seedlings (Dong et al. 2001), but the different tt mutants fail to produce any pigments under such conditions. As shown in Fig. 5, the anthocyanin pigmentation in tt5, tt6, tt3 and tt18 mutants was restored by the overexpression of SbCHI, SbF3H1 or SbF3H2, SbDFR1 or SbDFR3, and SbANS, respectively. Hence, our transgenic complementation analysis demonstrated that these sorghum genes all encode functional flavonoid enzymes in planta.

Fig. 5

Complementation analysis of sorghum flavonoid structural genes in transgenic Arabidopsis tt mutants. Anthocyanin pigmentation was restored in the transgenic tt5, tt6, tt3 and tt18 mutants overexpressing SbCHI, SbF3H1 or SbF3H2, SbDFR1 or SbDFR3, and SbANS, respectively. Seedlings were grown in low nitrogen medium to induce the anthocyanin biosynthesis pathway.

Fig. 5

Complementation analysis of sorghum flavonoid structural genes in transgenic Arabidopsis tt mutants. Anthocyanin pigmentation was restored in the transgenic tt5, tt6, tt3 and tt18 mutants overexpressing SbCHI, SbF3H1 or SbF3H2, SbDFR1 or SbDFR3, and SbANS, respectively. Seedlings were grown in low nitrogen medium to induce the anthocyanin biosynthesis pathway.

During the phenotypic investigations of the transgenic tt3 plants, more intense anthocyanin pigmentation was observed in the lines overexpressing SbDFR1 than in those overexpressing SbDFR3 (Fig. 5). Methanol extracts were then prepared from 2-week-old seedlings of three independent transformant lines for each sorghum transgene. Acid hydrolysis was performed to release the anthocyanidin (cyanidin) for quantification. As shown in Fig. 6, the tt3 + SbDFR1 plants accumulated approximately three times the amount of anthocyanin detected in the tt3 + SbDFR3 plants, suggesting that SbDFR1 is a more effective DFR enzyme for the biosynthesis of anthocyanin pigments in planta. On the other hand, no 3-deoxyanthocyanidins were detected in all the transgenic Arabidopsis extracts.

Fig. 6

(A) Quantitative analysis of anthocyanidin in acid-hydrolyzed extracts of transgenic Arabidopsis tt3 plants. Cyanidin was the major anthocyanidin detected in the plant samples. Data are expressed as average values of three transformant lines for each transgene, and error bars represent standard deviation. FW, fresh weight. (B) Semi-quantitative RT–PCR (27 PCR cycles) expression analyses of the SbDFR1 and SbDFR3 transgenes in the transformant lines used above.

Fig. 6

(A) Quantitative analysis of anthocyanidin in acid-hydrolyzed extracts of transgenic Arabidopsis tt3 plants. Cyanidin was the major anthocyanidin detected in the plant samples. Data are expressed as average values of three transformant lines for each transgene, and error bars represent standard deviation. FW, fresh weight. (B) Semi-quantitative RT–PCR (27 PCR cycles) expression analyses of the SbDFR1 and SbDFR3 transgenes in the transformant lines used above.

Enzyme activities of SbDFR1 and SbDFR3

From the gene expression analyses (Figs. 2–4), it is apparent that there is a specific DFR (i.e. SbDFR3) for the production of 3-deoxyanthocyanidin in sorghum seedlings following fungal inoculation and MeJA treatment. On the other hand, a different DFR (i.e. SbDFR1) is likely to be involved in the light-dependent anthocyanin pigmentation. We then investigated the enzyme activities of the two SbDFR proteins which were overexpressed in bacteria. The coding regions of SbDFR1 and SbDFR3 were subcloned into the pET28a vector and transformed into the Escherichia coli strain BL21. Soluble crude protein extracts were subsequently prepared from isopropyl-β-d-thiogalactopyranoside (IPTG)-induced cell cultures and the (His6)-tag SbDFR proteins purified for enzyme activity assays.

The recombinant proteins were tested on several common dihydroflavonol and flavanone substrates in the presence of NADPH. The enzyme activities were assayed at their optimum pH values and temperatures. The direct reaction products, flavan-3,4-diols (from dihydroflavonols) and flavan-4-ols (from flavanones), were converted by acid treatments to anthocyanidins and 3-deoxyanthocyanidins, respectively (Shimada et al. 2005), for liquid chromatography–mass spectrometry (LC-MS) detection and quantification. In general, both SbDFR1 and SbDFR3 were found to show substantially stronger activities toward dihydroflavonols (dihydrokaempferol and dihydroquercetin) than flavanones (naringenin and eriodictyol) (Fig. 7). Nevertheless, the presence of 3-deoxyanthocyanidins in the acid-treated flavanone reactions was positively confirmed by their retention times and MS/MS spectra. In all cases, anthocyanidins or 3-deoxyanthocyanidins were not detectable by LC-MS when no enzymes or boiled enzymes were included in the reactions.

Fig. 7

Enzyme activities of purified recombinant SbDFR1 and SbDFR3 proteins. After acid treatment, reaction products from dihydroflavonols and flavanones were converted to anthocyanidins and 3-deoxyanthocyanidins, respectively, for quantification in enzyme assays. Both proteins showed substantially higher activities toward dihydroflavonols than flavanones. No anthocyanidins or 3-deoxyanthocyanidins were detected in reactions containing no enzymes or boiled enzymes.

Fig. 7

Enzyme activities of purified recombinant SbDFR1 and SbDFR3 proteins. After acid treatment, reaction products from dihydroflavonols and flavanones were converted to anthocyanidins and 3-deoxyanthocyanidins, respectively, for quantification in enzyme assays. Both proteins showed substantially higher activities toward dihydroflavonols than flavanones. No anthocyanidins or 3-deoxyanthocyanidins were detected in reactions containing no enzymes or boiled enzymes.

Sequence analysis of DFR proteins

The four sorghum DFR proteins share at least 82% sequence identity. Phylogenetic analysis showed that DFR sequences from different plant species are separated according to their taxonomic groups (Fig. 8A). Thus, the sorghum sequences are closely related to the maize and rice DFRs. In addition, sequence alignment revealed the highly conserved N-terminal NADPH-binding region in all of the sorghum DFRs (Supplementary Fig. S1). The third residue (asparagine) within a 26 amino region proposed to be important for DFR substrate determination (Beld et al. 1989) was also identified in SbDFR1, SbDFR2 and SbDFR4 (Fig. 8B). DFR proteins having an aspartate residue in this position have been found to reduce dihydrokaempferol less effectively than the asparagine-type DFRs (Xie et al. 2004, Shimada et al. 2005). SbDFR3 contains a serine residue in this position (Fig. 8B) and was also shown to have slightly lower activities toward dihydrokaempferol when compared with SbDFR1 (Fig. 7).

Fig. 8

Sequence analysis of DFR proteins from sorghum and other plants. (A) An unrooted phylogenetic tree of different DFR proteins. The scale bar represents 0.05 substitutions per site. Mt, M. trunculata; Os, rice. (B) Partial alignment of the sorghum DFR proteins and selected sequences from the above tree. The 26 amino acid region proposed to determine substrate specificity is boxed. In the M. trunculata and lotus proteins, the indicated residue (N or D) is important for the utilization of DHK. The N-type DFRs were reported to reduce dihydroquercetin more effectively than the D-type. Most of the sorghum sequences are N-type DFRs, except for SbDFR3 which contains a serine residue in this position.

Fig. 8

Sequence analysis of DFR proteins from sorghum and other plants. (A) An unrooted phylogenetic tree of different DFR proteins. The scale bar represents 0.05 substitutions per site. Mt, M. trunculata; Os, rice. (B) Partial alignment of the sorghum DFR proteins and selected sequences from the above tree. The 26 amino acid region proposed to determine substrate specificity is boxed. In the M. trunculata and lotus proteins, the indicated residue (N or D) is important for the utilization of DHK. The N-type DFRs were reported to reduce dihydroquercetin more effectively than the D-type. Most of the sorghum sequences are N-type DFRs, except for SbDFR3 which contains a serine residue in this position.

Discussion

Sorghum is a valuable crop best known for its C4 metabolism, drought tolerance and potential as a biofuel source (Paterson 2008). The plant is also a rich source of distinct natural products, including dhurrin, sorgoleone and 3-deoxyanthocyanidins. The 3-deoxyanthocyanidins are rare pigmented flavonoids accumulated in floral tissues of sinningia, maize and sorghum. However, pathogen-inducible biosynthesis of 3-deoxyanthocyanidin phytoalexins occurs only in sorghum. Recent completion of the sorghum genome sequencing project has allowed us to identify specific flavonoid structural gene members which are responsive to inoculation with C. heterostrophus, a fungus known to elicit rapid and intense 3-deoxyanthocyanidin production in sorghum seedlings.

Analysis of the sorghum genome revealed the presence of nine CHS genes which are all located on chromosome 5, and three of them (SbCHS2a–SbCHS2c) are identical tandem repeats. In contrast to the large CHS gene family in sorghum, only two functional CHS genes (C2 and Whp) were reported in maize (Franken et al. 1991). A common feature of gene families is that individual members are differentially regulated in response to environmental or developmental signals. Using the sorghum mesocotyl inoculation system, we demonstrated that the expressions of most gene members, i.e. SbCHS1–SbCHS4, SbCHS6 and SbCHS7, were only inducible by pathogen inoculation under our experimental conditions. On the other hand, SbCHS5 was up-regulated following either light exposure or fungal inoculation. CHS is a plant-specific polyketide synthase that catalyzes the committed reaction step leading to the formation of different flavonoid metabolites (Dixon and Paiva 1995). Multiplications of the pathogen- inducible CHS genes in sorghum may reflect an evolutionary adaptation for the de novo synthesis of defense-related flavonoid metabolites.

The biosynthesis of anthocyanin pigments is one of the best characterized secondary metabolic pathways in plants. Starting with flavanones as substrates, the production of anthocyanidins takes place through sequential reactions catalyzed by F3H, DFR and ANS. Similarly, light-induced expression of SbF3H1, SbF3H2, SbDFR1 and SbANS was detected in sorghum DK46 mesocotyls during the accumulation of anthocyanin pigments (Fig. 2). All these genes were demonstrated to encode functional flavonoid enzymes by transgenic analysis in the corresponding Arabidopsis tt mutants (Fig. 5). On the other hand, reduction of F3H activity has been suggested to be a key factor for directing the flow of carbon to 3-deoxyflavonoid biosynthesis (Halbwirth et al. 2003, Winefield et al 2005). Consistently, expression of the functional F3H genes, SbF3H1 and SbF3H2, was not detected in sorghum seedlings during the light-independent fungal- or MeJA-induced 3-deoxyanthocyanidin biosynthesis (Figs, 2, 4). In addition, these light-inducible genes were transcriptionally down- regulated when DK46 seedlings were exposed to both stimuli of light and fungal inoculation (Fig. 3). Under the above circumstances, the levels of dihydroflavonols, which are converted from flavanones by F3H, are expected to be effectively reduced. This is particularly important since the sorghum DFR proteins were found to have substantially higher in vitro activities for dihydroflavonols than flavanones (Fig. 7).

Recombinant SbDFR1 and SbDFR3 showed low but detectable NADPH-dependent activities toward naringenin and eriodictyol (Fig. 7). Hence, biochemically, both sorghum enzymes are able to participate in 3-deoxyanthocyanidin biosynthesis through the reduction of flavanones, although they may not be the most preferred substrates under normal physiological conditions. On the other hand, it is clearly evident that SbDFR3 is specifically responsive to conditions that stimulate 3-deoxyanthocyanidin biosynthesis in sorghum, such as fungal inoculation (Figs. 2, 3) or MeJA treatment (Fig. 4). Evidence for the existence of a multienzyme assembly in flavonoid biosynthesis has been provided for Arabidopsis (Winkel 2004). Hence, the sorghum pathogen/stress-inducible flavonoid enzymes, without the involvement of F3H, may form a macromolecular complex that facilitates the conversion of flavanones to flavan-4-ols by SbDFR3, thereby allowing more efficient metabolite channeling for 3-deoxyanthocyandin phytoalexin production. The remaining step for the conversion of flavan-4-ols to 3-deoxyanthocyanidins is still uncharacterized. The corresponding reaction for anthocyanidin formation is catalyzed by ANS, which is a member of the family of 2-oxoglutarate-dependent oxygenases (DOXs) (Winkel-Shirley 2001). However, since the single-copy ANS gene (SbANS) is not expressed during fungal or MeJA-induced 3-deoxyanthocyanidin accumulation, an independent pathogen- or stress-responsive DOX gene with low homology to SbANS may instead be involved in the final step of the 3-deoxyanthocyaindin pathway.

There have been very few reports on the regulation of flavonoid biosynthesis in sorghum. In maize, P1 is a MYB regulatory protein controlling the accumulation of 3-deoxyflavonoids in floral tissues. Thus, P1 activates a subset of flavonoid structural genes encoding CHS, CHI and ANS, but not F3H (Grotewold et al. 1994, Grotewold et al. 1998). Recently, Y1 was reported to represent a sorghum P1 homolog which determines pericarp pigmentation resulting from phlobaphene and 3-deoxyanthocyanidin accumulation (Boddu et al. 2006). The cultivar BTx623 harbors a deletion Y1 allele and produces seeds without these 3-deoxyflavonoid pigments (Boddu et al. 2005). However, since inoculated BTx623 plants are able to synthesize apigeninidin and its methyl ether (Lo et al. 1999), a different regulatory mechanism is likely to be responsible for the activation of 3-deoxyanthocyanidin phytoalexin production. In this study, we also demonstrated that the pathogen-specific 3-deoxyanthocyanidin accumulation and SbDFR3 expression could be induced in roots by MeJA treatment but its effects were antagonized by SA (Fig. 4). Similarly, SA and MeJA co-treatment was previously shown to reduce the fold induction of 18 MeJA-induced genes by >25% in sorghum seedlings within 27 h (Salzman et al. 2005). The antagonistic effect of SA on jasmonate (JA)-inducible genes is well documented in Arabidopsis. For example, expression of the JA-responsive marker genes PDF1.2, LOX2 and VSP2 was strongly suppressed by biological or chemical induction of the SA pathway (Koornneef et al. 2008). Cross-talk between SA and JA signaling pathways is believed to play a key role in the fine-tuning of inducible defenses in plants (Reymond and Farmer 1998). Whether JA and SA are also involved as a signal for regulating the pathogen-inducible 3-deoxyanthocyanidin biosynthesis in sorghum remains to be elucidated. Further dissection of the remaining enzymatic step and the molecular regulatory network in 3-deoxyanthocyanidin biosynthesis will be facilitated by our identification of the pathogen-inducible SbDFR3 gene and the recent publication of the complete sorghum genome sequence.

Materials and Methods

Sorghum growth, fungal inoculation and chemical treatment conditions

Seeds of the sorghum cultivars (BTx623, DK46 and DK18) used in this study were former collections of the late Professor Ralph L. Nicholson of Purdue University (West Lafayette, IN, USA). Sorghum seeds were planted in rolls of germination paper and kept in the dark for 4 d as described previously (Lo et al. 1996). Etiolated seedlings were then placed under constant light at room temperature. For inoculation experiments, plants were sprayed with conidial suspensions of C. heterostrophus at 5.5 × 104 conidia ml−1 with Tween-20 as a wetting agent (100 μl 100 ml−1). The inoculated plants were incubated at 100% relative humidity (24 h) and kept in the dark at room temperature. For chemical treatments, the rolls of sorghum seedlings (4 d old) were placed in distilled water supplemented with SA, MeJA or SA + MeJA. Stock solutions of SA and MeJA (Sigma) were added to final concentrations of 1 mM and 100 μM, respectively, as described previously for treatments of sorghum seedlings at similar stages (Salzman et al. 2005).

RT–PCR experiments

Total RNA was extracted from sorghum mesocotyl tissues using the Trizol method (Invitrogen, CA, USA). DNase I-treated RNA samples (4 μg) were reversed transcribed by M-MLV reverse transcriptase (Promega, WI, USA). Gene-specific primers were designed from the 3′-untranslated regions of the different sorghum flavonoid structural genes. Amplification of target cDNA for semi-quantitative analysis was performed with the GoTaq Flexi DNA Taq polymerase (Promega, WI, USA) using the following program: 94°C (10 min); 28 cycles of 94°C (30 s), 55°C (30 s), 72°C (1 min); and 72°C (7 min). To obtain full-length coding regions of SbCHI, SbF3H1, SbF3H2, SbDFR1, SbDFR3 and SbANS for the complementation analyses described below, Pfx DNA polymerase (Invitrogen) was used for high-fidelity amplifications using the same program.

For quantitative gene expression analysis, real-time PCR was performed with the DNA Masterplus SYBR Green I kit (Roche Applied Science) using the LightCycler Instrument (Roche). The PCR program was as follows: pre-incubation (95°C for 10 min), amplification (95°C for 10 s, 60°C for 9 s, 72°C for 4 s with a single fluorescence measurement, 45 cycles), melting curve analysis (56–95°C with a heating rate of 0.1°C s−1 and a continuous fluorescence measurement) and cooling (40°C for 30 s). PCR products were confirmed by agarose gel (2%) electrophoresis and their identities verified by sequencing. Experiments were performed in triplicate for each sample. Relative expression ratios of the target genes were calculated essentially as described previously (Pfaffl et al. 2002).

A list of primers used in the different RT–PCR experiments described above is given in Supplementary Table S1.

Arabidopsis complementation analysis

The Arabidopsis tt3, tt5, tt6 and tt18 mutants (Arabidopsis Biological Resources Center, Columbus, OH, USA) defective in genes encoding DFR, CHI, F3H and ANS, respectively, were used for transgenic complementation analyses. Coding regions of the selected sorghum flavonoid genes were cloned into an overexpression vector (Yu et al. 2005) containing the cauliflower mosaic virus (CaMV) 35S promoter and the nopaline synthase 3′ terminator. The resulting plasmids were introduced into the binary vector pCAMBIA 1300 (CAMBIA, Australia). Agrobacterium-mediated transformation of the appropriate Arabidopsis mutants was performed by the floral dip method (Clough and Bent 1998). Harvested seeds were surface-sterilized and germinated on Murashige and Skoog (MS) (Sigma) agar plates containing 3% (v/v) sucrose and 25 μg ml−1 hygromycin (Sigma). Resistant seedlings were transplanted and placed in a growth chamber (22°C; 16 h light, 8 h dark). At least three independent lines with strong transgene expression for each construct were selected for phenotypic analysis. To induce anthocyanin accumulation, seeds were germinated on MS plates without nitrogen sources. For analysis of anthocyanidins by HPLC (see below), plant tissues (0.5–1.0 g) were collected from 7-day-old T1 seedlings, extracted in 100% methanol, followed by acid hydrolysis in 1% hydrochloric acid at 95°C for 30 min.

Heterologous expression of recombinant SbDFR proteins in bacteria

Full-length coding regions of SbDFR1 and SbDFR3 amplified from sorghum cDNA prepared as described above were subcloned in-frame with the (His)6-tag in the pET28a vector (Novagen). The final constructs were transformed into E. coli BL21 competent cells. SbDFR protein expression was induced by the addition of 1 mM IPTG to the bacterial cultures for 2 h at 25°C. Escherichia coli cells were harvested by centrifugation at 9,400 × g for 3 min, followed by washing in 0.1 M Tris–HCl (pH 7.5) containing 10 mM EDTA and 50 mM sucrose. The cell pellet was then suspended in 0.1 M potassium phosphate buffer (pH 7.0) containing 10% (w/v) sucrose, sonicated in ice, and centrifuged to collect the supernatant for purification through an affinity column of Ni-NTA agarose (Qiagen) according to the manufacturer’s instructions. After elution, the (His)6-tag DFR fusion proteins were concentrated by centrifugation in Microcon YM-3 (3,000 Da molecular weight cut-off) spin columns (Millipore). Protein purity was examined by SDS–gel electrophoresis.

In vitro enzyme assay of recombinant SbDFR1 and SbDFR3

For enzyme assays, the reaction mixtures contained 0.1 M Tris–HCl buffer (pH 7.0), 2 mM NADPH, 100 μM dihydroflavonol (dihydrokaempferol and dihydroquercetin, Sigma) or flavanone (naringenin and eriodictyol, Sigma) substrates in final volumes of 500 μl. Reactions were initiated by the addition of 10 μg of purified proteins and terminated by extraction with 500 μl of ethyl acetate (twice) after incubation at 25°C for 1 h. The ethyl acetate extracts were evaporated in vacuo at room temperature. The residues were dissolved in 100 μl of 5% hydrochloric acid in n-butanol and boiled for 1 h. Filtered samples (20 μl) were injected onto a HP 1100 series HPLC system (Agilent Technologies) connected to a Nucleosil 100-5 C18 column (5 μm, 150 × 2 mm, Agilent Technologies). Separation was performed using a solvent system of 0.5% formic acid (v/v) (A) and acetonitrile (B) with a gradient of 15–60% B over 25 min at a flow rate of 0.2 ml min−1. The LC elution was analyzed by an on-line API2000-QTrap mass spectrometer (Applied Biosystems) operating in multiple- reaction monitoring (MRM) mode (positive ionization). Transition reactions of pelargonidin (271.2→121.1), cyanidin (287.2→137.1), apigeninidin (255.2→171.2) and luteolinidin (271.2→115.1) were monitored and the LC-MRM peak areas used for concentration determination. Authentic standards of anthocyanidins and 3-deoxyanthocyanidins (Extrasynthese) were used for compound identification and quantification.

Sequence analysis

Sequences of different DFR proteins retrieved from GenBank were aligned by the ClustalW method (www.ebi.ac.uk/clustalw). The alignment was used to construct a phylogenetic tree by the Neighbor–Joining method in the MEGA4 program using the default parameters from the results of 1,000 bootstrap replicates (Kumar et al. 2004). Gene accession numbers for the amino acid sequences of DFRs are: Lotus japonicus DFR1, BAE19948; L. japonicus DFR2, BAE19949; L. japonicus DFR5, BAE19953; Arabidopsis TT4, BAA85261; Sinningia cardinalis DFR, AAR01565; rice OsDFR1, BAA36183; Medicago trunculata MtDFR1, AAR27014; M. trunculata MtDFR2, AAR27015; maize A1, P51108; Malus domestica DFR, AAO39816.

Supplementary data

Supplementary data are available at PCP online.

Funding

This work was supported by the Research Grants Council of the Hong Kong Special Administrative Region, China [grant Nos. HKU7527/06M and HKU 3/07C]; the HKU Seed Funding Program [200911159094].

Abbreviations

    Abbreviations
  • ANS

    anthocyanidin synthase

  • CHS

    chalcone synthase

  • CHI

    chalcone isomerase

  • DFR

    dihydroflavonol 4-reductase

  • DOX

    2-oxoglutarate-dependent thiogalactopyranoside

  • JA

    jasmonic acid

  • LC-MS

    liquid chromatography–mass spectrometry

  • Me-JA

    methyl jasmonate

  • MRM

    multiple-reaction monitoring

  • MS

    Murashige and Skoog

  • MS/MS

    tandem mass spectrometry

  • RT–PCR

    reverse transcription–PCR

  • SA

    salicylic acid.

The nucleotide sequence reported in this paper has been submitted to NCBI GenBank under the accession number GU320740 (SbF3H2).

Acknowledgments

The authors thank Dr J. S. T. Tsang (Biological Sciences, The University of Hong Kong) for access to their Roche LightCycler machine.

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