Genome-wide characterization of 2-oxoglutarate and Fe(II)-dependent dioxygenase family genes in tomato during growth cycle and their roles in metabolism

Background 2-Oxoglutarate and Fe(II)-dependent dioxygenases (2ODDs) belong to the 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily and are involved in various vital metabolic pathways of plants at different developmental stages. These proteins have been extensively investigated in multiple model organisms. However, these enzymes have not been systematically analyzed in tomato. In addition, type I flavone synthase (FNSI) belongs to the 2ODD family and contributes to the biosynthesis of flavones, but this protein has not been characterized in tomato. Results A total of 131 2ODDs from tomato were identified and divided into seven clades by phylogenetic classification. The Sl2ODDs in the same clade showed similar intron/exon distributions and conserved motifs. The Sl2ODDs were unevenly distributed across the 12 chromosomes, with different expression patterns among major tissues and at different developmental stages of the tomato growth cycle. We characterized several Sl2ODDs and their expression patterns involved in various metabolic pathways, such as gibberellin biosynthesis and catabolism, ethylene biosynthesis, steroidal glycoalkaloid biosynthesis, and flavonoid metabolism. We found that the Sl2ODD expression patterns were consistent with their functions during the tomato growth cycle. These results indicated the significance of Sl2ODDs in tomato growth and metabolism. Based on this genome-wide analysis of Sl2ODDs, we screened six potential FNSI genes using a phylogenetic tree and coexpression analysis. However, none of them exhibited FNSI activity. Conclusions Our study provided a comprehensive understanding of the tomato 2ODD family and demonstrated the significant roles of these family members in plant metabolism. We also suggest that no FNSI genes in tomato contribute to the biosynthesis of flavones. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07434-3.

Background 2-Oxoglutarate-dependent dioxygenases (2OGDs) are soluble, nonheme iron-containing enzymes and constitute the second-largest enzyme family in plants; these enzymes have a highly conserved but not ubiquitous HX(D/E) XnH triad motif in their 2OG-FeII_Oxy (PF03171) domain [1]. The amino acid sequences of plant 2OGD members are highly divergent and can be divided into different types. Analysis of the genomes of six model plant species showed that more than 500 putative 2OGDs could be classified into three major classes: DOXAs, DOXBs and DOXCs [2]. DOXA class enzymes, including plant homologs of Escherichia coli (E.coli) AlkB, are involved in the oxidative demethylation of alkylated nucleic acids and histones [3]. Prolyl 4hydroxylase homologs belonging to the DOXB class are involved in proline 4-hydroxylation in cell wall synthesis [4]. Unlike DOXA and B enzymes, which are limited to basic cell functions, DOXC enzymes largely participate in plant primary and secondary metabolism. The functionally characterized DOXC enzymes are involved in several conserved pathways, including hormone metabolism and specific pathways leading to the production of steroidal glycoalkaloids and flavonoids [1]. 2-Oxoglutarate and Fe(II)-dependent dioxygenases (2ODDs) constitute the specific DOXC subfamily and are involved in specialized plant metabolism [5]. In addition to having the classic 2OG-FeII_Oxy (PF03171) domain, they also have the conserved DIOX_ N(PF14226) domain [2].
Plants can synthesize massive amount of metabolites due to the diverse biosynthesis-related genes that encode different enzymes [6]. 2ODDs participate in various important metabolic pathways and directly affect the growth, development, and stress responses of plants. Several 2ODDs have been reported to be involved in melatonin metabolism and subsequently affect plant responses to cold, heat, salt, drought, and heavy metal stress and to pathogen invasion [7,8]. With respect to important plant hormones, such as auxin, ethylene, gibberellin, and salicylic acid, 2ODDs participate in pathways involving their biosynthesis and metabolism [1]. 2ODDs are also involved in the biosynthesis of secondary metabolites that have substantial biological and medicinal value. One 2ODD was identified to promote the biosynthesis of glucoraphasatin in radish [9]. Moreover, a genome-wide study of Salvia miltiorrhiza found that 2ODD plays a crucial role in the biosynthesis of tanshinones [10], and 2ODDs in tobacco (Nicotiana tabacum) have been functionally characterized as being involved in the biosynthesis of colorful flavonoids [11].
With more than 10,000 known structures, flavonoids are important secondary metabolites [12]. The diverse biological functions of flavonoids in plants as well as their various roles in interactions with other organisms offer many potential applications, from plant breeding to ecology, agriculture, and health benefits for humans [13,14]. The biosynthesis pathway of flavonoids in the Solanaceae has been extensively studied [15,16]. However, the crucial flavone synthase (FNS) enzymes have not been identified. To date, there are two types of enzymes known to catalyze flavone synthesis in higher plants [17]: FNSIs, a group of soluble 2ODDs, are mainly present in the Apiaceae [18], and FNSIIs, a group of NADPH-and molecular oxygen-dependent membranebound CYP monooxygenases, are widely distributed across the plant kingdom [19,20]. OsFNSI was identified using parsley FNSI as bait and is the first FNSI found outside of the Apiaceae family [21]. A putative ZmFNSI (Zea mays) enzyme has subsequently been found [22]. In addition, the Arabidopsis homolog of ZmFNSI also exhibits FNS activity [22]. FNSI is present not only in higher plants but also in liverworts. An FNSI has also been isolated and characterized from Plagiochasma appendiculatum [23]. In summary, FNSI is no longer confined to the Apiaceae family.
Tomato (Solanum lycopersicum), whose fruits are among the most popular fruits worldwide, has become an important source of micronutrients for the human diet and is widely cultivated around the world. Tomato fruits are consumed fresh or as processed products, such as canned tomatoes, paste, puree, ketchup, and juice. In addition to the commercial value of tomato, this species has been studied as a model plant due to its short life cycle and self-compatibility. Tomato plants produce many important primary and secondary metabolites, which can serve as intermediates or substrates for producing valuable new compounds. These advantages make tomato an excellent choice for metabolic engineering to produce important metabolites [24,25].
A comprehensive analysis of the 2ODD family in tomato has not been performed. In our current study, the Sl2ODDs that belong to the DOXC class were systematically analyzed for their phylogenetic evolution, gene structure, conserved motifs, chromosome location, gene duplications and metabolic pathway involvement. In addition, we verified the potential function of SlFNSI in flavonoid metabolism. Our results offer new insight into the function of 2ODDs in tomato and establish a knowledge base for further genetic improvement of tomato.

Results and discussion
Genome-wide identification and phylogenetic analysis of 2ODDs in tomato To investigate 2ODDs involved in plant metabolism, we focused our research on the DOXC subfamily of 2ODDs. A total of 131 putative tomato 2ODDs were found using BLAST and verified using HMMER searches. They all contained two conserved domains, 2OG-FeII_Oxy and DIOX_N. The number of amino acid residues of the predicted Sl2ODDs ranged from 248 to 418, with corresponding molecular weights from 28.4 to 47.7 kDa (Table S1). A phylogenetic tree was constructed to determine the relationships among these Sl2ODDs. The Sl2ODDs could be divided into seven clades (1-7) (Fig. 1). Clade 7 was the largest clade, with 32 members of Sl2ODDs, followed by clade 3, with 27 members. There were 25, 22, 11, and 10 members in clade 1, clade 2, clade 5, and clade 6, respectively. Clade 4 was the smallest, with only four Sl2ODD members. All reported tomato gibberellin oxidases (GAOXs) belonged to clade 1 [26][27][28]. In addition, 1-aminocyclopropane-1-carboxylic acid oxidases (ACOs) that involved in ethylene biosynthesis were enriched in clade 3 [29]. Taken together, these results showed that our method for retrieving Sl2ODDs is reliable and that our phylogenetic analysis was accurate enough for used in the estimation of the function of several unknown genes. For instance, twenty of the 25 members in clade 1 are GAOXs (Fig. 1), indicating that the remaining five members may also present GAOX activity.
Gene structure and protein motif analysis of Sl2ODDs To gain further insight into the structural diversity of tomato 2ODDs, we used the online software GSDS 2.0 to analyze the exon-intron structure of 2ODDs based on the genome sequence and the corresponding coding DNA sequences of the 2ODDs in tomato (Fig. 2c). The Sl2ODDs had 1~12 exons and could be divided into five categories based on exon number (Fig. 2d). Only Solyc00g031030 (0.7%) contained one exon. Twenty-two (16%), fifty-five (43%), and forty-two (32%) Sl2ODDs contained two, three and four exons, respectively. Eleven (8.3%) members had more than five exons. Notably, the genes from the same clade displayed similar exon Fig. 1 Phylogenetic analysis of tomato 2ODDs. Sl2ODD protein sequences were aligned using MEGA7.0 and evolutionary relationships were determined using Neighbor-Joining tree analysis with 1000 bootstrap replicates. Sl2ODDs fell in seven separate subfamilies named as clade 1-7 and each clade was colored numbers (Fig. 2). We identified 15 conserved motifs (1-15) using the online software MEME (Fig. 2b). Motifs 1-8 and 10-11 were widely distributed. Moreover, motifs 9, 12, 13, 14 and 15 were specifically distributed in different clades. The Sl2ODDs within the same clade were found to have similar motif compositions. Overall, the conserved motif composition and gene structure of the 2ODD members, together with the phylogenetic tree results, strongly supported the classification reliability.

Chromosomal distribution and synteny analysis of Sl2ODDs
The 128 Sl2ODD members (excluding Solyc00g031030, Solyc10g026520, and Solyc03g095920, which are identified using the MicroTom Metabolic Network (MMN) dataset based on ITAG 3.0 but absent in the updated ITAG 4.0 gene models) are widely distributed across the 12 tomato chromosomes. Chromosome 2 has the largest number of Sl2ODDs (25/128). Chromosome 5 and chromosome 11 contain only three Sl2ODDs. Most Sl2ODDs are located at the proximate or distal end of chromosomes (Fig. 3a). During the progress of plant evolution, gene duplication events contribute significantly to the generation and expansion of gene families. Gene duplication events were also identified for Sl2ODDs. We detected duplicated genes in the Sl2ODD family using the MCScanX package. Fiftyfour (42%) Sl2ODDs were confirmed to be tandemly duplicated genes (Fig. S1). We calculated the ka/ks ratios for all tandem genes that were almost less than one, indicating that purifying selection was the main force for 2ODD family gene evolution in tomato (Table S2). According to previously defined criteria [30], a chromosomal region within 200 kb containing two or more genes is defined as the tandem duplication event. Based on the physical location, gene clusters were found on chromosomes 2, 9 and 11 ( Fig. 3a), which indicated that tandem gene duplication events happened. However, no further specific functions of these genes were determined. In addition, elven pairs of Sl2ODDs were found to be segmental duplicates with the MCScanX method (Fig. 3b). Overall, these results indicated that some Sl2ODDs were possibly generated by tandem duplication and segmental duplication events.

Expression pattern of Sl2ODDs
To dissect the potential roles of Sl2ODDs involved in specific plant secondary metabolism, the expression patterns of Sl2ODD genes were investigated using the recently published MMN dataset [25]. Seven genes (Solyc02g038808, Solyc02g068315, Solyc02g071500, Solyc09g009105, Solyc09g010020, Solyc10g032565 and Solyc10g044447) were not found in the MMN, and two genes (Solyc05g052740 and Solyc12g013780) were not expressed. The expression patterns of the remaining 122 Sl2ODDs could be divided into four clusters (Fig. 4). The most obvious cluster contained 26 Sl2ODDs specifically expressed in mature fruit (Br15), including Solyc09g008560 and Solyc06g060070 which encode ACOs involved in ethylene biosynthesis. A total of 46 Sl2ODDs were mainly expressed in the flowering stage (F45) and the roots. Among them, SlANS (anthocyanidin synthase) (Solyc10g076660) exhibited abundant expression at F45 and was responsible for the synthesis of anthocyanins contributing to the color formation of flowers [31]. Twenty-two Sl2ODDs showed high expression levels during fruit development after the breaker (Br) stage, which is the key stage of fruit ripening. E8 (Solyc09g089580), a fruit-specific gene, was a member exhibiting this expression pattern. The last 28 Sl2ODDs did not show a particularly consistent expression trend. Interestingly, the expression patterns of some Sl2ODDs within the same clade were similar; for example, nearly half of the clade 3 genes (13/27) were expressed significantly in the roots. Similar phenomena occurred for Potential roles of Sl2ODDs in metabolism 2ODDs have been reported to facilitate numerous oxidation reactions such as hydroxylation, halogenation, desaturation, epimerization, cyclization and ring formation, ring cleavage, rearrangement, and demethylation [5,32]. The impressive versatility of 2ODDs highlights their importance in normal organismal function and has led to high-value specialized metabolites. To describe their potential roles in biosynthesis pathways, the key Sl2ODDs involved in metabolic pathways were analyzed in detail.

Gibberellin biosynthesis and catabolism
The plant hormones gibberellins (GA) regulate many plant development stages, including seed germination, cell and shoot elongation, leaf expansion, the transition to flowering, flower growth, and fruit development [33]. In this study, combined with data from published reports [2,26,28,34], we summarized and mapped the gibberellin synthesis and metabolic pathways (Fig. 5c). The well-defined GA biosynthesis and catabolism pathways include three types of GAOXs (GA20OXs, GA3OXs, GA2OXs) that belong to the 2ODD family and contribute to structural modification. GA biosynthesis can occur through two parallel pathways: non-13hydroxylation and 13-hydroxylation. Carbon-19 (C − 19 ) and carbon-20 (C-20) GAs are two types of substates for GAOXs (Fig. 5b). GA20OXs catalyze the successive oxidation and decarboxylation of C-20 GAs (GA12, GA53) at the C-20 position to form C-19 GAs (GA9, GA20). GA3OXs catalyze the hydroxylation of GA9 and GA20 at the C-3 position to form bioactive GA4 and GA1, respectively. GA2OXs play a role in GA catabolism responsible for GA deactivation via C-2 hydroxylation of the GA backbone. In the present study, a total of 19 putative GAOX coding genes, including 5 GA20OXs, 3 GA3OXs, and 11 GA2OXs, were found in the tomato genome (Fig. 5c).
The expression of SlGAOXs had obvious tissue specificity corresponding to significant expression in the roots, stems, flowers, and fruits (Fig. 5a). GA20OX1-3 and GA3OX1-2 expression levels have been previously reported [35] and are essentially consistent with our results. In particular, GA20OX2 was highly expressed in flower buds (F30), and GA3OX1 was highly expressed at F45 (when 50% of flowers reached anthesis) indicating that the expression of all of them is highly regulated during flower development [35]. Eleven GA2OXs were found in tomato, and their expression patterns differed among the different developmental stages and tissues. Overexpression of GA2OX1 resulted in the reduction in endogenous GAs and led to a decrease in tomato germination rate and fruit weight [26]. The expression patterns of GA2OX5 and GA2OX11 are similar to that of GA2OX1, and they may jointly regulate the development of tomato fruits and seeds. As GAs have a broad impact on plant growth, according to the expression profile, the different GA2OX homologs in tomato may function in different tissues and periods of plants.

Ethylene biosynthesis
Ethylene output by organs increases dramatically at specific stages of the plant growth cycle, such as fertilization, ripening, senescence, abscission, and response to stresses [36]. To determine the effect of 2ODDs on ethylene biosynthesis, we mapped the ethylene synthesis pathway (Fig. 6b). Ethylene is derived from the amino acid methionine (MET), catalyzed by AdoMet synthetase and 1-aminocyclopropane-1-carboxylic acid (ACC) synthase, to provide ACC precursors. ACC is then converted into ethylene by ACO, a member of the 2ODD family.
The expression model of the seven ACOs during tomato fruit development has been reported previously [29]. We further established the expression profile of ACOs throughout the growth cycle using MMN data (Fig. 6a). ACO1 was mainly expressed in the fruits, suggesting the well-known regulatory effect of ethylene on fruit ripening [29]. ACO3 and ACO4 regulate petal senescence and are significantly expressed in flowers (F45), as reported previously [37]. The expression patterns of seven ACOs were different, indicating that their roles in the plant may be diverse.

Steroidal glycoalkaloid (SGA) biosynthesis
Steroidal glycoalkaloids and their derivatives, mainly αtomatine and dehydrotomatine, are cytotoxic antinutritional compounds and accumulate in immature tomato fruits [38]. Cholesterol is the proposed common precursor for the biosynthesis of SGAs. A series of GLYCOAL-KALOID METABOLISM (GAME) genes are responsible for the hydroxylation, oxidation, and transamination of SGAs (Fig. 7b). Two of them, GAME11 and GAME31, are 2ODDs. GAME11 participates in the initial synthesis process of SGAs and was highly expressed in the roots, leaves, flowers, and immature green fruits (Fig. 7a). In contrast, GAME31 was mainly expressed at the tomato fruit ripening stage and catalyzes the first important step in the chemical shift after maturation within nonbitter SGA by a hydroxylation reaction [39,40]. Interestingly, we found that the different expression patterns between GAME11 and GAME31 resulted in the appropriate function at the right time. To gain further insight into the spatiotemporal specificities of compounds in different tissues, the coexpression of metabolites and genes was analyzed (Fig. 7a). The upstream SGA metabolites accumulated mainly in the leaves (L45) and green fruits, which is in line with the expression pattern of the upstream biosynthesis-related gene GAME11. The content of downstream SGAs decreases gradually after the Br period along with the expression of the downstream biosynthesis-related gene GAME31. These results are consistent with those of a previous study [40].

Flavonoid biosynthesis and metabolism
As shown in Fig. 8b, flavonoids are derived from the shikimate pathway, and the committed steps are catalyzed by chalcone synthase (CHS) and chalcone isomerase (CHI) to yield naringenin, which is subsequently modified by different enzymes, including cytochrome P450s (CYPs) and 2ODDs. FNSI, F3H, flavonol synthase (FLS), and anthocyanidin synthase (ANS) are flavonoid dioxygenases and belong to the 2ODD family. Based on the MMN data, we conducted a coexpression analysis of genes and compounds of the flavonoid pathway. Flavonoid 3′-hydroxylase (F3'H), CHI-like (CHIL), CHS-1, CHS-2, F3H, and FLS exhibited similar expression patterns during the tomato growth cycle. The accumulation of their corresponding products, such as eriodictyol and quercetin, followed (Fig. 8a). These results suggested that performing a coexpression analysis might be a reliable approach to study gene function.
Although the flavonoid pathway of plants has been studied [15,16], the key enzyme FNS responsible for the production of flavones, which compose the largest subgroup of flavonoids, has not been reported in the Solanaceae thus far. Studies have showed conflicting results regarding the presence of flavones in Solanaceae species, including tomato [41][42][43][44]. To further determine whether type I flavone synthase (FNSI) exists in tomato, a total of six candidate genes (Solyc02g068310, Solyc05g018130, Solyc03g080190, Solyc06g073080) including both F3H (Solyc02g083860) and FLS (Solyc11g013110), were selected based on phylogenetic tree analysis and coexpression analysis (Fig. 9). Two candidates (Solyc03g080190 and Solyc06g073080) along with other FNSIs (ZmFNSI, OsFNSI, AtDMR6) were distributed in the same group (blue). The other four candidates, Solyc02g068310, Solyc05g018130, F3H, and FLS exhibited coexpression patterns together with those of the accumulation of upstream compounds (Fig. 9b). The expression of these six potential genes may lead to FNS activity in tomato.
We cloned and expressed these candidates to test their FNS ability by converting flavanone (eriodictyol, Eri) into the corresponding flavone (luteolin, Lut) (Fig. 10a). AgFNSI (Apium graveolens) was used as a positive control [18] and showed FNS activity. F3H converted Eri into the flavanonol product dihydroquercetin (Diq), and FLS converted Diq into quercetin (Que), as expected. However, these candidates did not show FNS activities ( Fig. 10a and b). Regarding the other candidate genes, none of them exhibited FNS activity. All six potential genes failed to present FNS activity.

Conclusions
In this study, a total of 131 2ODDs were identified in the tomato genome, and their phylogenetic relationships, The remaining enzymes use Eri as a substrate to verify the FNS activity structures, chromosomal locations, duplications, and expression patterns were investigated. We found that the Sl2ODDs within the same clades share a similar motif composition and structure, inferring that they may have the same conserved function. The expression profile suggested that Sl2ODDs were widely distributed in different tissues and stages, revealing their importance for normal organismal function during the tomato growth cycle. Our results highlighted their irreplaceable roles in the biosynthesis of gibberellins, ethylene, steroidal glycoalkaloids, and flavonoids. Importantly, we characterized six potential Sl2ODDs encoding FNSI and concluded that there was no functional FNSI in tomato. Our findings promote the understanding of the evolution and function of 2ODDs in tomato, and therefore provide a reference for further research, especially for the genetic improvement of the tomato flavonoid pathway.

Plant material and growth conditions
The seeds of Solanum lycopersicum cv MicroTom were purchased from PanAmerican Seed (Illinois, USA). The resulting plants were grown in a greenhouse under a 16 h light/8 h dark photoperiod, 24°C and under 60% humidity [45].

Phylogenetic analysis
A total of 131 identified tomato 2ODDs were used for multiple protein sequence alignments via ClustalW in MEGA 7.0 (https://www.megasoftware.net/) [49]. The alignment results were subsequently used to construct a phylogenetic tree using the neighbor-joining method with 1000 bootstrap replicates and complete deletion. The other parameters were set to the defaults. The phylogenetic tree was displayed with the online tool EvolView (https://evolgenius.info//evol-view-v2) [49].

Gene structure and conserved motif analysis
Gene structures were analyzed based on the full-length genome sequence using the online tool Gene Structure Display Server (GSDS) 2.0 (http://gsds.gao-lab.org/index. php) [50]. To identify conserved motifs, the MEME online website (https://meme.n-bcr.net/meme) [51] was used with the following parameters: maximum number of motifs, 15; optimum width of each motif, between 12 and 30 residues; and optional parameters, default values. The characteristics of the 2ODD structures with motif compositions were visualized by EvolView.

Expression patterns of Sl2ODDs
The MicroTom Metabolic Network (MMN), a hightemporal-resolution transcriptome and metabolome dataset that contains data from 20 different tissues and stages during the MicroTom growth cycle, was used to study the expression patterns of 2ODDs (https://www. sciencedirect.com/science/article/pii/S167420522030183 0) [25]. A heatmap of 2ODD expression was created and displayed using the R language program. Transcript abundance was calculated as fragments per kilobase of exon model per million mapped reads, and the resulting values were z-score transformed to normalize the gene expression levels.

Coexpression analysis
Coexpression analysis was conducted for 20 different time points/tissue samples by R software with the heatmap package. The normalized expression values of genes and metabolites were calculated by the z-score method which is a built-in standardized function of R software.

Clone and expression of potential SlFNSIs
The full-length CDSs of potential SlFNSIs were amplified using polymerase chain reaction (PCR) from cDNA in conjunction with primers designed based on the sequences obtained from the tomato genome database (https://solgenomics.net/). The CDSs were cloned into a pDONR207, sequenced, and subsequently recombined into pDEST17 vector through Gateway cloning [45]. The potential SlFNSIs were expressed in E.coli strain BL21 grown at 37°C in Luria-Bertani (LB) media containing 0.05 mg ml − 1 carbenicillin until the optical density at 600 nm reached 0.7-0.9. Recombinant proteins were expressed by induction with 0.5 mM isopropyl β-D-1thiogalactopyranoside (IPTG) for 18 h at 16°C. Cells from 40 ml of culture were harvested by centrifugation and resuspended in 3 ml of PBS buffer (pH 7.0) at 4°C. Afterward, cell lysis was performed using an ultrasonic homogenizer and the lysates were recovered by centrifugation (10,000 g) for 20 min [55].

In vitro enzyme assays
The potential crude SlFNSI enzymes were incubated together with 160 μM α-oxoglutarate, 50 μM ferrous sulfate, and 200 μM eriodictyol in a final volume of 100 μl of PBS buffer (pH 7.0) for 1 h at 30°C. The reaction was stopped by the addition of 400 μl of methanol. The mixture was then centrifuged at 20,000 g at 4°C for 10 min after which the supernatant was collected for measurements.