AmCYP76AD1 is highly expressed in a red-leaf cultivar of A. tricolor
A. tricolor cultivars are important leafy vegetables that display leaf colors ranging from red to green depending on the betalain content28. To elucidate the genetic factors that influence betalain pigment accumulation in red- and green-leaf cultivars of A. tricolor (hereafter referred to as AMR and AMG, respectively) (Fig. 1a, b, Supplementary Fig. S1a, b), specific primer pairs were designed based on available sequence information from the NCBI database or previously published studies to selectively examine the transcript levels of genes related to the betalain biosynthesis pathway by qRT-PCR (Supplementary Table S1). In 3-week-old A. tricolor, AmCYP76AD1 and AmPPO showed higher expression levels in AMR than in AMG (Fig. 1c). Notably, only AmCYP76AD1 exhibited a highly differential expression pattern, showing an ~200-fold difference between AMR and AMG. In contrast, AmDODA, AmcDOPA5GT, AmB5GT, AmUGT79B30-like 4, AmMYB1, AmADH, AmCATPO, and AmTyDC did not show a significant differential expression pattern between AMR and AMG (Fig. 1c). The highly differential expression pattern of AmCYP76AD1 between AMR and AMG was also observed in 4-week-old A. tricolor (Supplementary Fig. S1c). Moreover, as a key element in the initiation of the betalain biosynthesis pathway, AmCYP76AD1 transcript levels displayed a high correlation with betalain pigment contents (Fig. 2a, b). Further phylogenetic reconstruction and LOGO analysis revealed that AmCYP76AD1 belongs to the CYP76ADa clade (Fig. 2c, d), whose members possesses both the tyrosine hydroxylase and L-DOPA oxidase activities required for L-DOPA and cyclo-DOPA formation, respectively (Fig. 1d). These results suggest that the elevated expression of AmCYP76AD1 is necessary for betalain pigment accumulation, which leads to an obvious red-violet color in the leaves and stems of AMR, but not in those of AMG.
AmDODA exhibits a marginal level of L-DOPA 4,5-dioxygenase activity
Although candidate transcripts related to betalain biosynthesis were identified previously in A. tricolor30,31, their functional and enzymatic activities have not yet been characterized. To functionally characterize the enzyme activities of AmCYP76AD1, AmDODA, and AmcDOPA5GT in the core pathway of betalain biosynthesis (Fig. 1d), 35S promoter-driven cDNAs encoding C-terminal YFP- or FLAG (SFP)-tagged AmCYP76AD1, AmDODA, and AmcDOPA5GT were transiently coexpressed in N. benthamiana leaves by agroinfiltration. Upon expression, only a small amount of betalain pigment was produced in N. benthamiana leaves, which was barely detectable (Fig. 3a). In contrast, as a positive control, high production of betalain pigments with red-violet color was observed when the Beta vulgaris tyrosinase gene (BvCYP76AD1), the B. vulgaris L-DOPA 4,5-dioxygenase gene (BvDODAa1), and the Mirabilis jalapacyclo-DOPA 5-O-glucosyltransferase gene (MjcDOPA5GT), were coexpressed in N. benthamiana leaves (Fig. 3a). To elucidate the A. tricolor genes responsible for the negligible activity of betalain synthesis in transient analysis, a series of coinfiltration assays were carried out by replacing the positive control genes individually with AmCYP76AD1, AmDODA, and AmcDOPA5GT. The replacements of BvCYP76AD1 and MjcDOPA5GT by AmCYP76AD1 and AmcDOPA5GT, respectively, resulted in high amounts of betalain pigment production in N. benthamiana leaves (Fig. 3b). However, AmDODA failed to replace the function of BvDODAa1. The coexpression of BvCYP76AD1, AmDODA, and MjcDOPA5GT only produced marginal levels of betalain pigments, which were barely detectable (Fig. 3b). Together with the comparable levels of proteins detected by western blotting (Fig. 3c), these results suggest that the L-DOPA 4,5-dioxygenase activity of AmDODA is very low compared to that of BvDODAa1.
Two DODAa homologues are present in A. tricolor
Recently, a phylogenetic study of Caryophyllales suggested that at least two DODAa genes are present in betalain-pigmented species, including Amaranthushypochondriacus12. To identify the DODAa homologue exhibiting a high level of L-DOPA 4,5-dioxygenase activity in A. tricolor, the RNA sequencing of aerial tissues derived from AMR and AMG plants was performed on the Illumina HiSeq 4000 platform. Two transcript libraries of AMR and AMG were built from the high-quality reads through de novo assembly and functional annotation (Supplementary Table S2, S3). The relative abundance of transcripts between AMR and AMG was illustrated in an MA plot (Fig. 4a). In addition, the relevant genes involved in the synthesis of betalain pigments were identified through in silico analysis and further highlighted in the MA plot (Fig. 4a, Supplementary Table S4). As expected, only AmCYP76AD1 was expressed at a significantly higher level in AMR than in AMG (Fig. 4a). These results suggest that AmCYP76AD1 is the key enzyme responsible for betalain pigment accumulation in AMR and that the loss of AmCYP76AD1 expression in AMG results in the green color phenotype.
Additionally, two DODAa homologues, AmDODAa1 and AmDODAa2 (referred to as AmDODA), were recovered through in silico analysis (Supplementary Fig. S2, Table S4). This indicated that gene duplication has occurred at least once in the DODAa lineage of A. tricolor. A reduced phylogenetic tree of DODAa was further generated using AmDODAa1, AmDODAa2, and previously characterized DODAa homologues from B. vulgaris, Carnegiea gigantea, Chenopodium quinoa, Mesembryanthemum crystallinum, M. jalapa, Parakeelya mirabilis, and Stegnosperma halimifolium (Fig. 4b). Two clades, DODAa1 and DODAa2, were obtained, and each of them presented seven previously identified conserved residues that are functionally important for high and marginal activities of L-DOPA 4,5-dioxygenase, respectively (Fig. 4c). Among these sequences, AmDODAa1 belongs to the DODAa1 clade and contains seven residues (DDYNDEI) associated with high L-DOPA 4,5-dioxygenase activity; AmDODAa2 (AmDODA) belongs to the DODAa2 clade and contains seven residues (YGFKNNT) associated with marginal L-DOPA 4,5-dioxygenase activity. These results suggest that AmDODAa1 may exhibit the high level of L-DOPA 4,5-dioxygenase activity required for betalain pigment production in A. tricolor.
AmDODAa1, but not AmDODAa2, exhibits a high level of L-DOPA 4,5-dioxygenase activity
As a key step in betalain biosynthesis, L-DOPA 4,5-dioxygenase can convert L-DOPA into betalamic acid, the basic structural unit of all betalains1,32. To functionally characterize the L-DOPA 4,5-dioxygenase activity of AmDODAa1, AmDODAa1 was coexpressed with BvCYP76AD1 and MjcDOPA5GT by agroinfiltration. As a result, high production of betalain pigments was observed when comparable amounts of proteins were expressed in N. benthamiana leaves. (Fig. 3b, c). These results indicate that AmDODAa1, but not AmDODAa2, exhibits a high level of L-DOPA 4,5-dioxygenase activity, similar to that of BvDODAa1.
To verify enzyme activity in vitro, AmDODAa1 and AmDODAa2 were expressed as SUMO-fused recombinant proteins in an Escherichia coli expression system (Fig. 5a). Enzymatic reactions were conducted following the method described by Sasaki et al. (2009)32, in which crude extracts prepared from E. coli were used. After incubation for 5 min at 30°C, a bright yellow color derived from betalamic acid was observed in the reaction mixture containing L-DOPA, ascorbic acid, and a crude extract prepared from E. coli harboring AmDODAa1 or BvDODAa1, but not AmDODAa2 (Fig. 5b). However, only a very weak yellow color was observed when the reaction mixture contained twofold crude extract prepared from E. coli harboring AmDODAa2 (Fig. 5b). As a control, a reaction mixture containing the crude extract was prepared from E. coli harboring only the vector, and no color was observed (Fig. 5b). The reaction products were then subjected to LC-MS/MS analysis and revealed that the clear peak at a retention time of 7.5 min was betalamic acid (Fig. 5c). These results confirm that AmDODAa2 exhibits marginal levels of L-DOPA 4,5-dioxygenase activity.
Reconstruction of the core betalain biosynthesis pathway of A. tricolor in N. benthamiana
In this study, we also attempted to use TRV-based virus-induced gene silencing (VIGS) to examine the functional activities of genes involved in betalain biosynthesis in A. tricolor. However, the transient silencing of AmCYP76AD1 in A. tricolor was particularly challenging and failed in our hands. In addition, the attempted overexpression of AmCYP76AD1 to complement the betalain pigments in the leaves of AMG was unsuccessful using an agroinfiltration system. These differences might have resulted from the different varieties and low transformation efficiency of A. tricolor33.
To reconstruct the core betalain biosynthesis pathway of A. tricolor, AmCYP76AD1, AmDODAa1, and AmcDOPA5GT were transiently overexpressed in N. benthamiana leaves by agroinfiltration for the heterologous engineering of betalain pigments. Similar to the vector-only control, the heterologous expression of single AmCYP76AD1, AmDODAa1, or AmcDOPA5GT was not sufficient to produce any betalain pigment in N. benthamiana (Fig. 6a). However, low production of betalain pigments was observed when AmCYP76AD1 and AmDODAa1 were coexpressed in N. benthamiana (Fig. 6a). In contrast, no betalain pigment was observed when AmCYP76AD1 and AmcDOPA5GT or AmDODAa1 and AmcDOPA5GT were coexpressed in N. benthamiana (Fig. 6a). Only the coexpression of AmCYP76AD1, AmDODAa1, and AmcDOPA5GT together was sufficient to produce high amounts of betalain pigments in N. benthamiana, which resulted in a strong red-violet color (Fig. 6a). The strong red-violet color was similar to that in the positive control in which BvCYP76AD1, BvDODAa1, and MjcDOPA5GT were coexpressed in N. benthamiana (Fig. 6a). As expected, the coexpression of AmCYP76AD1, AmDODAa2, and AmcDOPA5GT only produced marginal levels of betalain pigments, which were barely detectable (Fig. 6a). Together with the comparable amount of proteins detected by western blotting (Fig. 6b), our results suggest that the enzyme activities of AmCYP76AD1, AmDODAa1, and AmDOPA5GT are sufficient to construct the core betalain biosynthesis pathway of A. tricolor.