A 2-oxoglutarate-dependent dioxygenase is integrated in DIMBOA-biosynthesis

Two Iron(II), α-Ketoglutarate-Dependent Enzymes Encoded by the PPZ Gene Cluster of Metarhizium majus Enable Production of 8-Hydroxyperamine

Entomopathogenic fungus Metarhizium majus contains the nine-gene PPZ cluster, with ppzA, encoding a peramine-producing nonribosomal peptide synthetase, as the central component. In this work, the roles of two α-ketoglutarate, iron-dependent oxygenases encoded by the PPZ genes ppzC and ppzD were elucidated. PpzD was found to produce both trans-4-hydroxy-l-proline and trans-3-hydroxy-l-proline in a 13.1:1 ratio, yielding a key precursor for peramine biosynthesis. PpzC was found to act directly on peramine, yielding the novel analogue 8-hydroxyperamine.

Genetic Variation, DIMBOA Accumulation, and Candidate Gene Identification in Maize Multiple Insect-Resistance

Maize seedlings contain high amounts of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA), and the effect of DIMBOA is directly associated with multiple insect-resistance against insect pests such as Asian corn borer and corn leaf aphids. Although numerous genetic loci for multiple insect-resistant traits have been identified, little is known about genetic controls regarding DIMBOA content. In this study, the best linear unbiased prediction (BLUP) values of DIMBOA content in two ecological environments across 310 maize inbred lines were calculated; and their phenotypic data and BLUP values were used for marker-trait association analysis. We identified nine SSRs that were significantly associated with DIMBOA content, which explained 4.30-20.04% of the phenotypic variation. Combined with 47 original genetic loci from previous studies, we detected 19 hot loci and approximately 11 hot loci (in Bin 1.04, Bin 2.00-2.01, Bin 2.03-2.04, Bin 4.00-4.03, Bin 5.03, Bin 5.05-5.07, Bin 8.01-8.03, Bin 8.04-8.05, Bin 8.06, Bin 9.01, and Bin 10.04 regions) supported pleiotropy for their association with two or more insect-resistant traits. Within the 19 hot loci, we identified 49 candidate genes, including 12 controlling DIMBOA biosynthesis, 6 involved in sugar metabolism/homeostasis, 2 regulating peroxidases activity, 21 associated with growth and development [(auxin-upregulated RNAs (SAUR) family member and v-myb avian myeloblastosis viral oncogene homolog (MYB)], and 7 involved in several key enzyme activities (lipoxygenase, cysteine protease, restriction endonuclease, and ubiquitin-conjugating enzyme). The synergy and antagonism interactions among these genes formed the complex defense mechanisms induced by multiple insect pests. Moreover, sufficient genetic variation was reported for DIMBOA performance and SSR markers in the 310 tested maize inbred lines, and 3 highly (DIMBOA content was 402.74-528.88 μg g^-1 FW) and 15 moderate (DIMBOA content was 312.92-426.56 μg g^-1 FW) insect-resistant genotypes were major enriched in the Reid group. These insect-resistant inbred lines can be used as parents in maize breeding programs to develop new varieties.

Plant metabolic gene clusters in the multi-omics era

Secondary metabolism in plants gives rise to a vast array of small-molecule natural products. The discovery of operon-like gene clusters in plants has provided a new perspective on the evolution of specialized metabolism and the opportunity to rapidly advance the metabolic engineering of natural product production. Here, we review historical aspects of the study of plant metabolic gene clusters as well as general strategies for identifying plant metabolic gene clusters in the multi-omics era. We also emphasize the exploration of their natural variation and evolution, as well as new strategies for the prospecting of plant metabolic gene clusters and a deeper understanding of how their structure influences their function.

Tomato E8 Encodes a C-27 Hydroxylase in Metabolic Detoxification of α-Tomatine during Fruit Ripening

Tomato (Solanum lycopersicum) contains α-tomatine, a steroidal glycoalkaloid that contributes to the plant defense against pathogens and herbivores through its bitter taste and toxicity. It accumulates at high levels in all the plant tissues, especially in leaves and immature green fruits, whereas it decreases during fruit ripening through metabolic conversion to the nontoxic esculeoside A, which accumulates in the mature red fruit. This study aimed to identify the gene encoding a C-27 hydroxylase that is a key enzyme in the metabolic conversion of α-tomatine to esculeoside A. The E8 gene, encoding a 2-oxoglutalate-dependent dioxygenase, is well known as an inducible gene in response to ethylene during fruit ripening. The recombinant E8 was found to catalyze the C-27 hydroxylation of lycoperoside C to produce prosapogenin A and is designated as Sl27DOX. The ripe fruit of E8/Sl27DOX-silenced transgenic tomato plants accumulated lycoperoside C and exhibited decreased esculeoside A levels compared with the wild-type (WT) plants. Furthermore, E8/Sl27DOX deletion in tomato accessions resulted in higher lycoperoside C levels in ripe fruits than in WT plants. Thus, E8/Sl27DOX functions as a C-27 hydroxylase of lycoperoside C in the metabolic detoxification of α-tomatine during tomato fruit ripening, and the efficient detoxification by E8/27DOX may provide an advantage in the domestication of cultivated tomatoes.

Increased benzoxazinoid (Bx) levels in wheat seedlings via jasmonic acid treatment and etiolation and their effects on Bx genes including Bx6

Wheat accumulates benzoxazinoid (Bx) as a defensive compound. While Bx occurs at high concentrations, particularly in the early growth stages, its mechanism of regulation remains unclear. In the present study, we first examined the effects of several plant hormones on Bx concentrations in wheat seedlings. Among the compounds tested, jasmonate (JA) elevated the concentrations of DIMBOA-Glc (2-β-D-glucoside of 2,4-dihydroxy-7-methoy-1,4-benzoxazin-3-one), the primary Bx species in intact wheat seedlings, without a significant increase in HDMBOA-Glc (4-O-methyl-DIMBOA-Glc), which is known to be upregulated by stresses. In addition, growing the plants in the dark increased DIMBOA-Glc levels. Quantification of the Bx-biosynthetic genes showed that TaBx8 (UDP-Glc:Bx glucosyltrasferase) was influenced by neither JA nor etiolation, indicating that TaBx8 is under the regulation mechanism distinct from the mechanisms influencing the others. In addition, none of the other gene expression patterns exhibited considerable correlation with DIMBOA-Glc accumulation. Since there was no correlation between transcript levels of the genes involved in Bx biosynthesis and Bx accumulation, other factors may control the levels of Bx in wheat. In the course of gene analyses, we isolated TaBx6, one of the last two genes that had not been identified in wheat in the DIMBOA-Glc biosynthetic pathway. All the four TaBx6 genes cloned in the present study were expressed in Escherichia coli and characterized their activity.

Benzoxazinoids selectively affect maize root-associated nematode taxa

Although the effects of plant secondary metabolites on plant defence have been studied for decades, the exact roles of secondary metabolites in shaping plant-associated microbial and nematode communities remain elusive. We evaluated the effects of benzoxazinoids, a group of secondary metabolites present in several cereals, on root-associated nematodes. We employed 18S rRNA metabarcoding to compare maize root-associated nematode communities in a bx1 knockout maize line impaired in benzoxazinoid synthesis and in its parental wild type. Both genotype and plant age affected the composition of the nematode community in the roots, and the effects of benzoxazinoids on nematode communities were stronger in the roots than in the rhizosphere. Differential abundance analysis and quantitative PCR showed that the root lesion nematode Pratylenchus neglectus was enriched in the bx1 mutant line, while another root lesion nematode, Pratylenchus crenatus, was reduced. Correlation analysis showed that benzoxazinoid concentrations in maize roots mostly correlated negatively with the relative abundance of nematode sequence reads. However, positive correlations between benzoxazinoids and nematode taxa, including several plant-parasitic nematodes, were also identified. Our detailed nematode community analysis suggests differential and selective effects of benzoxazinoids on soil nematodes depending on both the nematode species and the benzoxazinoid compound.

Benzoxazinoids Biosynthesis in Rye (Secale cereale L.) Is Affected by Low Temperature

Benzoxazinoids (BXs) are specialized metabolites with protective properties that are synthesized predominantly by Poaceae species, including rye (Secale cereale). Among factors known to influence BXs production, prolonged low temperature has not been studied previously. In this study, the influence of cultivation at 4 °C, which is essential for vernalization, on the concentration of BXs (HBOA, DIBOA, GDIBOA, DIMBOA, GDIMBOA, and MBOA) and the expression level of genes involved in the BX biosynthesis pathway (ScBx1–ScBx5 and ScIgl) in three rye inbred lines was investigated. After cultivation for seven weeks at 4 °C, the expression level of all analyzed genes and BX concentrations had decreased compared with those at the initiation of treatment (21 days after germination) in control and cold-treated plants. At this time point, the decrease in BX concentrations and gene expression was lower in cold-treated plants than in untreated plants. In contrast, at 77 days after germination, the gene expression levels and BX concentrations in untreated plants had generally increased. Investigation of the vernalization impact on rye BXs accumulation, as well as on Bx gene expression, may aid with determination of the most suitable winter lines and cultivars of rye for cultivation and breeding purposes.

Setaria viridis as a model for translational genetic studies of jasmonic acid-related insect defenses in Zea mays

Little is known regarding insect defense pathways in Setaria viridis (setaria), a model system for panicoid grasses, including Zea mays (maize). It is thus of interest to compare insect herbivory responses of setaria and maize. Here we use metabolic, phylogenetic, and gene expression analyses to measure a subset of jasmonic acid (JA)-related defense responses to leaf-chewing caterpillars. Phylogenetic comparisons of known defense-related maize genes were used to identify putative orthologs in setaria, and candidates were tested by quantitative PCR to determine transcriptional responses to insect challenge. Our findings show that while much of the core JA-related metabolic and genetic responses appear conserved between setaria and maize, production of downstream secondary metabolites such as benzoxazinoids and herbivore-induced plant volatiles are dissimilar. This diversity of chemical defenses and gene families involved in secondary metabolism among grasses presents new opportunities for cross species engineering. The high degree of genetic similarity and ease of orthologous gene identification between setaria and maize make setaria an excellent species for translational genetic studies, but the species specificity of downstream insect defense chemistry makes some pathways unamenable to cross-species comparisons.

Expanding the roles for 2-oxoglutarate-dependent oxygenases in plant metabolism

Covering: up to 2018 2-Oxoglutarate-dependent oxygenases (2ODOs) comprise a large enzyme superfamily in plant genomes, second in size only to the cytochromes P450 monooxygenase (CYP) superfamily. 2ODOs participate in both primary and specialized plant pathways, and their occurrence across all life kingdoms points to an ancient origin. Phylogenetic evidence supports substantial expansion and diversification of 2ODOs following the split from the common ancestor of land plants. More conserved roles for these enzymes include oxidation within hormone metabolism, such as the recently described capacity of Dioxygenase for Auxin Oxidation (DAO) for governing auxin homeostasis. Conserved structural features among 2ODOs has provided a basis for continued investigation into their mechanisms, and recent structural work is expected to illuminate intriguing reactions such as that of 1-aminocyclopropane-1-carboxylic acid oxidase (ACCO). Phylogenetic radiation among this superfamily combined with neo- and subfunctionalization has enabled recruitment to highly specialized pathways, including those yielding medicines, flavours, dyes, poisons, and compounds important for plant-environment interactions. Catalytic versatility of 2ODOs in plants and across broader taxa continues to inspire biochemists tasked with the discovery of new enzymes. This highlight article summarizes recent reports up to 2018 of 2ODOs within plant metabolism. Furthermore, the respective contributions of 2ODOs and other oxidases to natural product biosynthesis are discussed as a framework for continued discovery.

Maize synthesized benzoxazinoids affect the host associated microbiome

BACKGROUND

Plants actively shape their associated microbial communities by synthesizing bio-active substances. Plant secondary metabolites are known for their signaling and plant defense functions, yet little is known about their overall effect on the plant microbiome. In this work, we studied the effects of benzoxazinoids (BXs), a group of secondary metabolites present in maize, on the host-associated microbial structure. Using BX knock-out mutants and their W22 parental lines, we employed 16S and ITS2 rRNA gene amplicon analysis to characterize the maize microbiome at early growth stages.

RESULTS

Rhizo-box experiment showed that BXs affected microbial communities not only in roots and shoots, but also in the rhizosphere. Fungal richness in roots was more affected by BXs than root bacterial richness. Maize genotype (BX mutants and their parental lines) as well as plant age explained both fungal and bacterial community structure. Genotypic effect on microbial communities was stronger in roots than in rhizosphere. Diverse, but specific, microbial taxa were affected by BX in both roots and shoots, for instance, many plant pathogens were negatively correlated to BX content. In addition, a co-occurrence analysis of the root microbiome revealed that BXs affected specific groups of the microbiome.

CONCLUSIONS

This study provides insights into the role of BXs for microbial community assembly in the rhizosphere and in roots and shoots. Coupling the quantification of BX metabolites with bacterial and fungal communities, we were able to suggest a gatekeeper role of BX by showing its correlation with specific microbial taxa and thus providing insights into effects on specific fungal and bacterial taxa in maize roots and shoots. Root microbial co-occurrence networks revealed that BXs affect specific microbial clusters.

The PhytoClust tool for metabolic gene clusters discovery in plant genomes

The existence of Metabolic Gene Clusters (MGCs) in plant genomes has recently raised increased interest. Thus far, MGCs were commonly identified for pathways of specialized metabolism, mostly those associated with terpene type products. For efficient identification of novel MGCs, computational approaches are essential. Here, we present PhytoClust; a tool for the detection of candidate MGCs in plant genomes. The algorithm employs a collection of enzyme families related to plant specialized metabolism, translated into hidden Markov models, to mine given genome sequences for physically co-localized metabolic enzymes. Our tool accurately identifies previously characterized plant MGCs. An exhaustive search of 31 plant genomes detected 1232 and 5531 putative gene cluster types and candidates, respectively. Clustering analysis of putative MGCs types by species reflected plant taxonomy. Furthermore, enrichment analysis revealed taxa- and species-specific enrichment of certain enzyme families in MGCs. When operating through our web-interface, PhytoClust users can mine a genome either based on a list of known cluster types or by defining new cluster rules. Moreover, for selected plant species, the output can be complemented by co-expression analysis. Altogether, we envisage PhytoClust to enhance novel MGCs discovery which will in turn impact the exploration of plant metabolism.

Biosynthesis and chemical transformation of benzoxazinoids in rye during seed germination and the identification of a rye Bx6-like gene

Benzoxazinoids are secondary metabolites with plant defense properties and possible health-promoting effects in humans. In this study, the transcriptional activity of ScBx genes (ScBx1-ScBx5; ScBx6-like), involved in benzoxazinoid biosynthesis, was analyzed during germination and early seedling development in rye. Our results showed that ScBx genes had highest levels of expression at 24-30 h after germination, followed by a decrease at later stages. For ScBx1-ScBx5 genes expression was higher in shoots compared with root tissues and vice versa for ScBx6-like gene transcripts. Moreover, methylated forms of benzoxazinoids accumulated in roots rather than in shoots during seedling development, in particular reaching high levels of HMBOA-glc in roots. Chemical profiles of benzoxazinoid accumulation in the developing seedling reflected the combined effects of de novo biosynthesis of the compounds as well as the turnover of compounds either pre-stored in the embryo or de novo biosynthesized. Bioinformatic analysis, together with the differential distribution of ScBx6-like transcripts in root and shoot tissues, suggested the presence of a ZmBx6 homolog encoding a 2-oxoglutarate dependent dehydrogenase in rye. The ScBx6-like cDNA was expressed in E. coli for functional characterization in vitro. LC-MS/MS analysis showed that the purified enzyme was responsible for the oxidation of DIBOA-glc into TRIBOA-glc, strongly suggesting the ScBX6-like enzyme in rye to be a functional ortholog of maize ZmBX6.

Identification and VIGS-based characterization of Bx1 ortholog in rye (Secale cereale L.)

The first step of the benzoxazinoid (BX) synthesis pathway is catalyzed by an enzyme with indole-3-glycerol phosphate lyase activity encoded by 3 genes, Bx1, TSA and Igl. A gene highly homologous to maize and wheat Bx1 has been identified in rye. The goal of the study was to analyze the gene and to experimentally verify its role in the rye BX biosynthesis pathway as a rye ortholog of the Bx1 gene. Expression of the gene showed peak values 3 days after imbibition (dai) and at 21 dai it was undetectable. Changes of the BX content in leaves were highly correlated with the expression pattern until 21 dai. In plants older than 21 dai despite the undetectable expression of the analyzed gene there was still low accumulation of BXs. Function of the gene was verified by correlating its native expression and virus-induced silencing with BX accumulation. Barley stripe mosaic virus (BSMV)-based vectors were used to induce transcriptional (TGS) and posttranscriptional (PTGS) silencing of the analyzed gene. Both strategies (PTGS and TGS) significantly reduced the transcript level of the analyzed gene, and this was highly correlated with lowered BX content. Inoculation with virus-based vectors specifically induced expression of the analyzed gene, indicating up-regulation by biotic stressors. This is the first report of using the BSMV-based system for functional analysis of rye gene. The findings prove that the analyzed gene is a rye ortholog of the Bx1 gene. Its expression is developmentally regulated and is strongly induced by biotic stress. Stable accumulation of BXs in plants older than 21 dai associated with undetectable expression of ScBx1 indicates that the function of the ScBx1 in the BX biosynthesis is redundant with another gene. We anticipate that the unknown gene is a putative ortholog of the Igl, which still remains to be identified in rye.

Distribution of the tryptophan pathway-derived defensive secondary metabolites gramine and benzoxazinones in Poaceae

The Poaceae is a large taxonomic group consisting of approximately 12,000 species and is classified into 12 subfamilies. Gramine and benzoxazinones (Bxs), which are biosynthesized from the tryptophan pathway, are well-known defensive secondary metabolites in the Poaceae. We analyzed the presence or absence of garamine and Bxs in 64 species in the Poaceae by LC-MS/MS. We found that Hordeum brachyantherum and Hakonechloa macra accumulated gramine, but the presence of gramine was limited to small groups of species. We also detected Bxs in four species in the Pooideae and six species in the Panicoideae. In particular, four species in the Paniceae tribe in Panicoideae accumulaed Bxs, indicating that this tribe is a center of the Bx distribution. Bxs were absent in the subfamilies other than Pooideae and Panicoideae. These findings provide an overview of biased distribution of gramine and Bxs in Poaceae species.

Computational genomic identification and functional reconstitution of plant natural product biosynthetic pathways

Covering: 2003 to 2016The last decade has seen the first major discoveries regarding the genomic basis of plant natural product biosynthetic pathways. Four key computationally driven strategies have been developed to identify such pathways, which make use of physical clustering, co-expression, evolutionary co-occurrence and epigenomic co-regulation of the genes involved in producing a plant natural product. Here, we discuss how these approaches can be used for the discovery of plant biosynthetic pathways encoded by both chromosomally clustered and non-clustered genes. Additionally, we will discuss opportunities to prioritize plant gene clusters for experimental characterization, and end with a forward-looking perspective on how synthetic biology technologies will allow effective functional reconstitution of candidate pathways using a variety of genetic systems.

Plant metabolic clusters - from genetics to genomics

Contents 771 I. 771 II. 772 III. 780 IV. 781 V. 786 786 References 786 SUMMARY: Plant natural products are of great value for agriculture, medicine and a wide range of other industrial applications. The discovery of new plant natural product pathways is currently being revolutionized by two key developments. First, breakthroughs in sequencing technology and reduced cost of sequencing are accelerating the ability to find enzymes and pathways for the biosynthesis of new natural products by identifying the underlying genes. Second, there are now multiple examples in which the genes encoding certain natural product pathways have been found to be grouped together in biosynthetic gene clusters within plant genomes. These advances are now making it possible to develop strategies for systematically mining multiple plant genomes for the discovery of new enzymes, pathways and chemistries. Increased knowledge of the features of plant metabolic gene clusters - architecture, regulation and assembly - will be instrumental in expediting natural product discovery. This review summarizes progress in this area.

Prolonged expression of the BX1 signature enzyme is associated with a recombination hotspot in the benzoxazinoid gene cluster in Zea mays

Benzoxazinoids represent preformed protective and allelopathic compounds. The main benzoxazinoid in maize (Zea mays L.) is 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA). DIMBOA confers resistance to herbivores and microbes. Protective concentrations are found predominantly in young plantlets. We made use of the genetic diversity present in the maize nested association mapping (NAM) panel to identify lines with significant benzoxazinoid concentrations at later developmental stages. At 24 d after imbibition (dai), only three lines, including Mo17, showed effective DIMBOA concentrations of 1.5mM or more; B73, by contrast, had low a DIMBOA content. Mapping studies based on Mo17 and B73 were performed to reveal mechanisms that influence the DIMBOA level in 24 dai plants. A major quantitative trait locus mapped to the Bx gene cluster located on the short arm of chromosome 4, which encodes the DIMBOA biosynthetic genes. Mo17 was distinguished from all other NAM lines by high transcriptional expression of the Bx1 gene at later developmental stages. Bx1 encodes the signature enzyme of the pathway. In Mo17×B73 hybrids at 24 dai, only the Mo17 Bx1 allele transcript was detected. A 3.9kb cis-element, termed DICE (distal cis-element), that is located in the Bx gene cluster approximately 140 kb upstream of Bx1, was required for high Bx1 transcript levels during later developmental stages in Mo17. The DICE region was a hotspot of meiotic recombination. Genetic analysis revealed that high 24 dai DIMBOA concentrations were not strictly dependent on high Bx1 transcript levels. However, constitutive expression of Bx1 in transgenics increased DIMBOA levels at 24 dai, corroborating a correlation between DIMBOA content and Bx1 transcription.

Biosynthesis of the diterpenoid lycosantalonol via nerylneryl diphosphate in Solanum lycopersicum

We recently reported that three genes involved in the biosynthesis of monoterpenes in trichomes, a cis-prenyltransferase named neryl diphosphate synthase 1 (NDPS1) and two terpene synthases (TPS19 and TPS20), are present in close proximity to each other at the tip of chromosome 8 in the genome of the cultivated tomato (Solanum lycopersicum). This terpene gene “cluster” also contains a second cis-prenyltransferase gene (CPT2), three other TPS genes, including TPS21, and the cytochrome P450-oxidoreductase gene CYP71BN1. CPT2 encodes a neryneryl diphosphate synthase. Co-expression in E. coli of CPT2 and TPS21 led to the formation of the diterpene lycosantalene, and co-expression in E. coli of CPT2, TPS21 and CYP71BN1 led to the formation of lycosantalonol, an oxidation product of lycosantalene. Here we show that maximal expression of all three genes occurs in the petiolule part of the leaf, but little expression of these genes occurs in the trichomes present on the petiolules. While lycosantalene or lycosantalonol cannot be detected in the petiolules of wild-type plants (or anywhere else in the plant), lycosantalene and lycosantalonol are detected in petiolules of transgenic tomato plants expressing CPT2 under the control of the 35S CaMV promoter. These results suggest that lycosantalene and lycosantalonol are produced in the petiolules and perhaps in other tissues of wild-type plants, but that low rate of synthesis, controlled by the rate-limiting enzyme CPT2, results in product levels that are too low for detection under our current methodology. It is also possible that these compounds are further modified in the plant. The involvement of CPT2, TPS21 and CYP71BN1 in a diterpenoid biosynthetic pathway outside the trichomes, together with the involvement of other genes in the cluster in the synthesis of monoterpenes in trichomes, indicates that this cluster is further evolving into “sub-clusters” with unique biochemical, and likely physiological, roles.

Functional diversity of 2-oxoglutarate/Fe(II)-dependent dioxygenases in plant metabolism

Oxidative enzymes catalyze many different reactions in plant metabolism. Among this suite of enzymes are the 2-oxoglutarate/Fe(II)-dependent dioxygenases (2-ODDs). Cytochromes P450 (CYPs) as often considered the most versatile oxidative enzymes in nature, but the diversity and complexity of reactions catalyzed by 2-ODDs is superior to the CYPs. The list of oxidative reactions catalyzed by 2-ODDs includes hydroxylations, demethylations, desaturations, ring closure, ring cleavage, epimerization, rearrangement, halogenation, and demethylenation. Furthermore, recent work, including the discovery of 2-ODDs involved in epigenetic regulation, and others catalyzing several characteristic steps in specialized metabolic pathways, support the argument that 2-ODDs are among the most versatile and important oxidizing biological catalysts. In this review, we survey and summarize the pertinent literature with a focus on several key reactions catalyzed by 2-ODDs, and discuss the significance and impact of these enzymes in plant metabolism.

Evolution and diversity of the 2-oxoglutarate-dependent dioxygenase superfamily in plants

The 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily is the second largest enzyme family in the plant genome, and its members are involved in various oxygenation/hydroxylation reactions. Despite their biochemical significance in metabolism, a systematic analysis of plant 2OGDs remains to be accomplished. We present a phylogenetic classification of 479 2OGDs in six plant models, ranging from green algae to angiosperms. These were classified into three classes - DOXA, DOXB and DOXC - based on amino acid sequence similarity. The DOXA class includes plant homologs of Escherichia coli AlkB, which is a prototype of 2OGD involved in the oxidative demethylation of alkylated nucleic acids and histones. The DOXB class is conserved across all plant taxa and is involved in proline 4-hydroxylation in cell wall protein synthesis. The DOXC class is involved in specialized metabolism of various phytochemicals, including phytohormones and flavonoids. The vast majority of 2OGDs from land plants were classified into the DOXC class, but only seven from Chlamydomonas, suggesting that this class has diversified during land plant evolution. Phylogenetic analysis assigned DOXC-class 2OGDs to 57 phylogenetic clades. 2OGD genes involved in gibberellin biosynthesis were conserved among vascular plants, and those involved in flavonoid and ethylene biosynthesis were shared among seed plants. Several angiosperm-specific clades were found to be involved in various lineage-specific specialized metabolisms, but 31 of the 57 DOXC-class clades were only found in a single species. Therefore, the evolution and diversification of DOXC-class 2OGDs is partly responsible for the diversity and complexity of specialized metabolites in land plants.

2-Oxoglutarate: linking TCA cycle function with amino acid, glucosinolate, flavonoid, alkaloid, and gibberellin biosynthesis

The tricarboxylic acid (TCA) cycle intermediate 2-oxoglutarate (2-OG) is used as an obligatory substrate in a range of oxidative reactions catalyzed by 2-OG-dependent dioxygenases. These enzymes are widespread in nature being involved in several important biochemical processes. We have recently demonstrated that tomato plants in which the TCA cycle enzyme 2-OG dehydrogenase (2-ODD) was antisense inhibited were characterized by early senescence and modified fruit ripening associated with differences in the levels of bioactive gibberellin (GA). Accordingly, there is now compelling evidence that the TCA cycle plays an important role in modulating the rate of flux from 2-OG to amino acid metabolism. Here we discuss recent advances in the biochemistry and molecular biology of 2-OG metabolism occurring in different biological systems indicating the importance of 2-OG and 2-OG dependent dioxygenases not only in glucosinolate, flavonoid and alkaloid metabolism but also in GA and amino acid metabolism. We additionally summarize recent findings regarding the impact of modification of 2-OG metabolism on biosynthetic pathways involving 2-ODDs.

Proteomic investigation of response to FORL infection in tomato roots

Fusarium oxysporum f. sp. radicis-lycopersici (FORL) leading to fusarium crown and root rot is considered one of the most destructive tomato soilborne diseases occurring in greenhouse and field crops. In this study, response to FORL infection in tomato roots was investigated by differential proteomics in susceptible (Monalbo) and resistant (Momor) isogenic tomato lines, thus leading to identify 33 proteins whose amount changed depending on the pathogen infection, and/or on the two genotypes. FORL infection induced accumulation of pathogen-related proteins (PR proteins) displaying glucanase and endochitinases activity or involved in redox processes in the Monalbo genotype. Interestingly, the level of the above mentioned PR proteins was not influenced by FORL infection in the resistant tomato line, while other proteins involved in general response mechanisms to biotic and/or abiotic stresses showed significant quantitative differences. In particular, the increased level of proteins participating to arginine metabolism and glutathione S-transferase (GST; EC 2.5.1.18) as well as that of protein LOC544002 and phosphoprotein ECPP44-like, suggested their key role in pathogen defence.

Biosynthesis of the biphenyl phytoalexin aucuparin in Sorbus aucuparia cell cultures treated with Venturia inaequalis

Aucuparin is the most widely distributed biphenyl phytoalexin in the rosaceous subtribe Pyrinae, which includes the economically important fruit trees apple and pear. The biphenyl scaffold is formed by biphenyl synthase, which catalyzes biosynthesis of 3,5-dihydroxybiphenyl. Conversion of this precursor to aucuparin (3,5-dimethoxy-4-hydroxybiphenyl) was studied in cell cultures of Sorbus aucuparia after treatment with an elicitor preparation from the scab-causing fungus Venturia inaequalis. The sequence of the biosynthetic steps detected was O-methylation - 4-hydroxylation - O-methylation. The two alkylation reactions were catalyzed by distinct methyltransferases, which differed in pH and temperature optima as well as stability. Biphenyl 4-hydroxylase was a microsomal cytochrome P450 monooxygenase, whose activity was appreciably decreased by the addition of established P450 inhibitors. When fed to V. inaequalis-treated S. aucuparia cell cultures, radioactively labeled 3,5-dihydroxybiphenyl was not only incorporated into aucuparin but also into the dibenzofuran eriobofuran, the accumulation of which paralleled that of aucuparin. However, biphenyl 2'-hydroxylase activity proposed to be involved in dibenzofuran formation was detected in neither microsomes nor cell-free extracts in the presence of NADPH and 2-oxoglutarate, respectively. Nevertheless, a basis for studying biphenyl biosynthesis at the gene level is provided.

Benzoxazinoids in rye allelopathy - from discovery to application in sustainable weed control and organic farming

The allelopathic potency of rye (Secale cereale L.) is due mainly to the presence of phytotoxic benzoxazinones-compounds whose biosynthesis is developmentally regulated, with the highest accumulation in young tissue and a dependency on cultivar and environmental influences. Benzoxazinones can be released from residues of greenhouse-grown rye at levels between 12 and 20 kg/ha, with lower amounts exuded by living plants. In soil, benzoxazinones are subject to a cascade of transformation reactions, and levels in the range 0.5-5 kg/ha have been reported. Starting with the accumulation of less toxic benzoxazolinones, the transformation reactions in soil primarily lead to the production of phenoxazinones, acetamides, and malonamic acids. These reactions are associated with microbial activity in the soil. In addition to benzoxazinones, benzoxazolin-2(3H)-one (BOA) has been investigated for phytotoxic effects in weeds and crops. Exposure to BOA affects transcriptome, proteome, and metabolome patterns of the seedlings, inhibits germination and growth, and can induce death of sensitive species. Differences in the sensitivity of cultivars and ecotypes are due to different species-dependent strategies that have evolved to cope with BOA. These strategies include the rapid activation of detoxification reactions and extrusion of detoxified compounds. In contrast to sensitive ecotypes, tolerant ecotypes are less affected by exposure to BOA. Like the original compounds BOA and MBOA, all exuded detoxification products are converted to phenoxazinones, which can be degraded by several specialized fungi via the Fenton reaction. Because of their selectivity, specific activity, and presumably limited persistence in the soil, benzoxazinoids or rye residues are suitable means for weed control. In fact, rye is one of the best cool season cover crops and widely used because of its excellent weed suppressive potential. Breeding of benzoxazinoid resistant crops and of rye with high benzoxazinoid contents, as well as a better understanding of the soil persistence of phenoxazinones, of the weed resistance against benzoxazinoids, and of how allelopathic interactions are influenced by cultural practices, would provide the means to include allelopathic rye varieties in organic cropping systems for weed control.

Making new molecules - evolution of pathways for novel metabolites in plants

Plants have adapted to their environments by diversifying in various ways. This diversification is reflected at the phytochemical level in their production of numerous specialized secondary metabolites that provide protection against biotic and abiotic stresses. Plant speciation is therefore intimately linked to metabolic diversification, yet we do not currently have a deep understanding of how new metabolic pathways evolve. Recent evidence indicates that genes for individual secondary metabolic pathways can be either distributed throughout the genome or clustered, but the relative frequencies of these two pathway organizations remain to be established. While it is possible that clustering is a feature of pathways that have evolved in recent evolutionary time, the answer to this and how dispersed and clustered pathways may be related remain to be addressed. Recent advances enabled by genomics and systems biology are beginning to yield the first insights into network evolution in plant metabolism. This review focuses on recent progress in understanding the evolution of clustered and dispersed pathways for new secondary metabolites in plants.

Phylogenomics of the benzoxazinoid biosynthetic pathway of Poaceae: gene duplications and origin of the Bx cluster

Background

The benzoxazinoids 2,4-dihydroxy-1,4-benzoxazin-3-one (DIBOA) and 2,4-dihydroxy-7- methoxy-1,4-benzoxazin-3-one (DIMBOA), are key defense compounds present in major agricultural crops such as maize and wheat. Their biosynthesis involves nine enzymes thought to form a linear pathway leading to the storage of DI(M)BOA as glucoside conjugates. Seven of the genes (Bx1-Bx6 and Bx8) form a cluster at the tip of the short arm of maize chromosome 4 that includes four P450 genes (Bx2-5) belonging to the same CYP71C subfamily. The origin of this cluster is unknown.

Results

We show that the pathway appeared following several duplications of the TSA gene (α-subunit of tryptophan synthase) and of a Bx2-like ancestral CYP71C gene and the recruitment of Bx8 before the radiation of Poaceae. The origins of Bx6 and Bx7 remain unclear. We demonstrate that the Bx2-like CYP71C ancestor was not committed to the benzoxazinoid pathway and that after duplications the Bx2-Bx5 genes were under positive selection on a few sites and underwent functional divergence, leading to the current specific biochemical properties of the enzymes. The absence of synteny between available Poaceae genomes involving the Bx gene regions is in contrast with the conserved synteny in the TSA gene region.

Conclusions

These results demonstrate that rearrangements following duplications of an IGL/TSA gene and of a CYP71C gene probably resulted in the clustering of the new copies (Bx1 and Bx2) at the tip of a chromosome in an ancestor of grasses. Clustering favored cosegregation and tip chromosomal location favored gene rearrangements that allowed the further recruitment of genes to the pathway. These events, a founding event and elongation events, may have been the key to the subsequent evolution of the benzoxazinoid biosynthetic cluster.

A 2-oxoglutarate-dependent dioxygenase from Ruta graveolens L. exhibits p-coumaroyl CoA 2'-hydroxylase activity (C2'H): a missing step in the synthesis of umbelliferone in plants

Coumarins are important compounds that contribute to the adaptation of plants to biotic or abiotic stresses. Among coumarins, umbelliferone occupies a pivotal position in the plant phenylpropanoid network. Previous studies indicated that umbelliferone is derived from the ortho-hydroxylation of p-coumaric acid by an unknown biochemical step to yield 2,4-dihydroxycinnamic acid, which then undergoes spontaneous lactonization. Based on a recent report of a gene encoding a 2-oxoglutarate-dependent dioxygenase from Arabidopsis thaliana that exhibited feruloyl CoA 6'-hydroxylase activity (Bourgaud et al., 2006), we combined a bioinformatic approach and a cDNA library screen to identify an orthologous ORF (Genbank accession number JF799117) from Ruta graveolens L. This ORF shares 59% amino acid identity with feruloyl CoA 6'-hydroxylase, was functionally expressed in Escherichia coli, and converted feruloyl CoA into scopoletin and p-coumaroyl CoA into umbelliferone with equal activity. Its bi-functionality was further confirmed in planta: transient expression of JF799117 in Nicotiana benthamiana yielded plants with leaves containing high levels of umbelliferone and scopoletin when compared to control plants, which contained barely detectable traces of these compounds. The expression of JF799117 was also tightly correlated to the amount of umbelliferone that was found in UV-elicited R. graveolens leaves. Therefore, JF799117 encodes a p-coumaroyl CoA 2'-hydroxylase in R. graveolens, which represents a previously uncharacterized step in the synthesis of umbelliferone in plants. Psoralen, which is an important furanocoumarin in R. graveolens, was found to be a competitive inhibitor of the enzyme, and it may exert this effect through negative feedback on the enzyme at an upstream position in the pathway.

Dispersed benzoxazinone gene cluster: molecular characterization and chromosomal localization of glucosyltransferase and glucosidase genes in wheat and rye

Benzoxazinones (Bxs) are major defensive secondary metabolites in wheat (Triticum aestivum), rye (Secale cereale), and maize (Zea mays). Here, we identified full sets of homeologous and paralogous genes encoding Bx glucosyltransferase (GT) and Bx-glucoside glucosidase (Glu) in hexaploid wheat (2n = 6x = 42; AABBDD). Four GT loci (TaGTa-TaGTd) were mapped on chromosomes 7A, 7B (two loci), and 7D, whereas four glu1 loci (Taglu1a-Taglu1d) were on chromosomes 2A, 2B (two loci), and 2D. Transcript levels differed greatly among the four loci; B-genome loci of both TaGT and Taglu1 genes were preferentially transcribed. Catalytic properties of the enzyme encoded by each homeolog/paralog also differed despite high levels of identity among amino acid sequences. The predominant contribution of the B genome to GT and Glu reactions was revealed, as observed previously for the five Bx biosynthetic genes, TaBx1 to TaBx5, which are separately located on homeologous groups 4 and 5 chromosomes. In rye, where the ScBx1 to ScBx5 genes are dispersed to chromosomes 7R and 5R, ScGT and Scglu were located separately on chromosomes 4R and 2R, respectively. The dispersal of Bx-pathway loci to four distinct chromosomes in hexaploid wheat and rye suggests that the clustering of Bx-pathway genes, as found in maize, is not essential for coordinated transcription. On the other hand, barley (Hordeum vulgare) was found to lack the orthologous GT and glu loci like the Bx1 to Bx5 loci despite its close phylogenetic relationship with wheat and rye. These results contribute to our understanding of the evolutionary processes that the Bx-pathway loci have undergone in grasses.

From hormones to secondary metabolism: the emergence of metabolic gene clusters in plants

Gene clusters for the synthesis of secondary metabolites are a common feature of microbial genomes. Well-known examples include clusters for the synthesis of antibiotics in actinomycetes, and also for the synthesis of antibiotics and toxins in filamentous fungi. Until recently it was thought that genes for plant metabolic pathways were not clustered, and this is certainly true in many cases; however, five plant secondary metabolic gene clusters have now been discovered, all of them implicated in synthesis of defence compounds. An obvious assumption might be that these eukaryotic gene clusters have arisen by horizontal gene transfer from microbes, but there is compelling evidence to indicate that this is not the case. This raises intriguing questions about how widespread such clusters are, what the significance of clustering is, why genes for some metabolic pathways are clustered and those for others are not, and how these clusters form. In answering these questions we may hope to learn more about mechanisms of genome plasticity and adaptive evolution in plants. It is noteworthy that for the five plant secondary metabolic gene clusters reported so far, the enzymes for the first committed steps all appear to have been recruited directly or indirectly from primary metabolic pathways involved in hormone synthesis. This may or may not turn out to be a common feature of plant secondary metabolic gene clusters as new clusters emerge.

Comparative proteomic analysis provides new insights into mulberry dwarf responses in mulberry (Morus alba L.)

Mulberry dwarf (MD) is a serious infectious disease of mulberry caused by phytoplasma. Infection with MD phytoplasma results in stress phenotypes of yellowing, phyllody, stunting, proliferation, and witches' broom. Physiological and biochemical analysis has shown that infection with MD phytoplasma causes an increase in soluble carbohydrate and starch content, and a decrease in the net photosynthesis rate, carboxylation efficiency, and pigment content of leaves. Furthermore, damage to the chloroplast ultrastructure was detected in infected leaves. To better understand the pathogen-stress response of mulberry (Morus alba L.) to MD phytoplasma, we conducted a comparative proteomic analysis using 2-DE of infected and healthy leaves. Among 500 protein spots that were reproducibly detected, 20 were down-regulated and 17 were up-regulated. MS identified 16 differentially expressed proteins. The photosynthetic proteins rubisco large subunit, rubisco activase, and sedoheptulose-1,7-bisphosphatase showed enhanced degradation in infected leaves. Based these results, a model for the occurrence mechanism of MD is proposed. In conclusion, this study provides new insights into the mulberry response to MD phytoplasma infection.

Genetic variation at bx1 controls DIMBOA content in maize

The main hydroxamic acid in maize (Zea mays L.) is 2-4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA). DIMBOA confers resistance to leaf-feeding by several corn borers. Most genes involved in the DIMBOA metabolic pathway are located on the short arm of chromosome 4, and quantitative trait loci (QTLs) involved in maize resistance to leaf-feeding by corn borers have been localized to that region. However, the low resolution of QTL linkage mapping does not allow convincing proof that genetic variation at bx loci was responsible for the variability for resistance. This study addressed the following objectives: to determine the QTLs involved in DIMBOA synthesis across genetically divergent maize inbreds using eight RIL families from the nested association mapping population, to check the stability of QTLs for DIMBOA content across years by evaluating two of those RIL families in 2 years, and to test the involvement of bx1 by performing association mapping with a panel of 281 diverse inbred lines. QTLs were stable across different environments. A genetic model including eight markers explained approximately 34% of phenotypic variability across eight RIL families and the position of the largest QTL co-localizes with the majority of structural genes of the DIMBOA pathway. Candidate association analysis determined that sequence polymorphisms at bx1 greatly affects variation of DIMBOA content in a diverse panel of maize inbreds, but the specific causal polymorphism or polymorphisms responsible for the QTL detected in the region 4.01 were not identified. This result may be because the causal polymorphism(s) were not sequenced, identity is masked by linkage disequilibrium, adjustments for population structure reduce significance of causal polymorphisms or multiple causal polymorphisms affecting bx1 segregate among inbred lines.

Operons

Operons (clusters of co-regulated genes with related functions) are common features of bacterial genomes. More recently, functional gene clustering has been reported in eukaryotes, from yeasts to filamentous fungi, plants, and animals. Gene clusters can consist of paralogous genes that have most likely arisen by gene duplication. However, there are now many examples of eukaryotic gene clusters that contain functionally related but non-homologous genes and that represent functional gene organizations with operon-like features (physical clustering and co-regulation). These include gene clusters for use of different carbon and nitrogen sources in yeasts, for production of antibiotics, toxins, and virulence determinants in filamentous fungi, for production of defense compounds in plants, and for innate and adaptive immunity in animals (the major histocompatibility locus). The aim of this article is to review features of functional gene clusters in prokaryotes and eukaryotes and the significance of clustering for effective function.

Benzoxazinoid biosynthesis, a model for evolution of secondary metabolic pathways in plants

Benzoxazinoids are secondary metabolites that are effective in defence and allelopathy. They are synthesised in two subfamilies of the Poaceae and sporadically found in single species of the dicots. The biosynthesis is fully elucidated in maize; here the genes encoding the enzymes of the pathway are in physical proximity. This "biosynthetic cluster" might facilitate coordinated gene regulation. Data from Zea mays, Triticum aestivum and Hordeum lechleri suggest that the pathway is of monophyletic origin in the Poaceae. The branchpoint from the primary metabolism (Bx1 gene) can be traced back to duplication and functionalisation of the alpha-subunit of tryptophan synthase (TSA). Modification of the intermediates by consecutive hydroxylation is catalysed by members of a cytochrome P450 enzyme subfamily (Bx2-Bx5). Glucosylation by an UDP-glucosyltransferase (UGT, Bx8, Bx9) is essential for the reduction of autotoxicity of the benzoxazinoids. In some species 2,4-dihydroxy-1,4-benzoxazin-3-one-glucoside (DIBOA-glc) is further modified by the 2-oxoglutarate-dependent dioxygenase BX6 and the O-methyltransferase BX7. In the dicots Aphelandra squarrosa, Consolida orientalis, and Lamium galeobdolon, benzoxazinoid biosynthesis is analogously organised: The branchpoint is established by a homolog of TSA, P450 enzymes catalyse hydroxylations and at least the first hydroxylation reaction is identical in dicots and Poaceae, the toxic aglucon is glucosylated by an UGT. Functionally, TSA and BX1 are indole-glycerolphosphate lyases (IGLs). Igl genes seem to be generally duplicated in angiosperms. Modelling and biochemical characterisation of IGLs reveal that the catalytic properties of the enzyme can easily be modified by mutation. Independent evolution can be assumed for the BX1 function in dicots and Poaceae.

Rediscovering the bioactivity and ecological role of 1,4-benzoxazinones

Compounds of the (2H)-1,4-benzoxazin-3(4H)-one class have attracted the attention of phytochemists since the first isolation of 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one (DIBOA) and 2,4-dihydroxy-7-methoxy-(2H)-1,4-benzoxazin-3(4H)-one (DIMBOA). Extensive research has been carried out on the isolation and synthesis of these materials as well as on the dynamics of their degradation in different systems. This has led to the discovery of a wide variety of compounds that are of high interest from the point of view of phytotoxic, antifungal, antimicrobial, and antifeedant effects among others. The potential application of benzoxazinones and their derivatives as leads for natural herbicide models is a topic of current interest. Furthermore, the importance of degradation on the ecological behaviour of benzoxazinone-producing plants is also being realised, and proposals concerning the role of the degradation products in chemical defence mechanisms have been put forward. There is also increasing interest in the improvement of analytical methodologies, and ecotoxicologic effects, toxicity on target and non-target organisms, and degradation kinetics are also being addressed. The development of new phytotoxicity bioassay techniques represents one of the most important breakthroughs in this respect. Moreover, benzoxazinones and some of their derivatives have been employed in the development of pharmaceuticals. The versatility of the benzoxazinone skeleton, in addition to its relative chemical simplicity and accessibility, makes these chemicals amongst the most promising sources of bioactive compounds that are natural in origin.

Hydroxamic acids derived from 2-hydroxy-2H-1,4-benzoxazin-3(4H)-one: key defense chemicals of cereals

Many cereals accumulate hydroxamic acids derived from 2-hydroxy-2H-1,4-benzoxazin-3(4H)-one. These benzoxazinoid hydroxamic acids are involved in defense of maize against various lepidopteran pests, most notably the European corn borer, in defense of cereals against various aphid species, and in allelopathy affecting the growth of weeds associated with rye and wheat crops. The role of benzoxazinoid hydroxamic acids in defense against fungal infection is less clear and seems to depend on the nature of the interactions at the plant-fungus interface. Efficient use of benzoxazinoid hydroxamic acids as resistance factors has been limited by the inability to selectively increase their levels at the plant growth stage and the plant tissues where they are mostly needed for a given pest. Although the biosynthesis of benzoxazinoid hydroxamic acids has been elucidated, the genes and mechanisms controlling their differential expression in different plant tissues and along plant ontogeny remain to be unraveled.

beta-Glucosidases as detonators of plant chemical defense

Some plant secondary metabolites are classified as phytoanticipins. When plant tissue in which they are present is disrupted, the phytoanticipins are bio-activated by the action of beta-glucosidases. These binary systems--two sets of components that when separated are relatively inert--provide plants with an immediate chemical defense against protruding herbivores and pathogens. This review provides an update on our knowledge of the beta-glucosidases involved in activation of the four major classes of phytoanticipins: cyanogenic glucosides, benzoxazinoid glucosides, avenacosides and glucosinolates. New aspects of the role of specific proteins that either control oligomerization of the beta-glucosidases or modulate their product specificity are discussed in an evolutionary perspective.

Elucidation of the final reactions of DIMBOA-glucoside biosynthesis in maize: characterization of Bx6 and Bx7

Benzoxazinoids were identified in the early 1960s as secondary metabolites of the grasses that function as natural pesticides and exhibit allelopathic properties. Benzoxazinoids are synthesized in seedlings and stored as glucosides (glcs); the main aglucone moieties are 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one (DIBOA) and 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA). The genes of DIBOA-glc biosynthesis have previously been isolated and the enzymatic functions characterized. Here, the enzymes for conversion of DIBOA-glc to DIMBOA-glc are identified. DIBOA-glc is the substrate of the dioxygenase BENZOXAZINLESS6 (BX6) and the produced 2,4,7-trihydroxy-2H-1,4-benzoxazin-3-(4H)-one-glc is metabolized by the methyltransferase BX7 to yield DIMBOA-glc. Both enzymes exhibit moderate K(m) values (below 0.4 mm) and k(cat) values of 2.10 s(-1) and 0.25 s(-1), respectively. Although BX6 uses a glucosylated substrate, our localization studies indicate a cytoplasmic localization of the dioxygenase. Bx6 and Bx7 are highest expressed in seedling tissue, a feature shared with the other Bx genes. At present, Bx6 and Bx7 have no close relatives among the members of their respective gene families. Bx6 and Bx7 map to the cluster of Bx genes on the short arm of chromosome 4.

cis-Jasmone induces accumulation of defence compounds in wheat, Triticum aestivum

Liquid phase extraction (LPE) and vapor phase extraction (VPE) methodologies were used to evaluate the impact of the plant activator, cis-jasmone, on the secondary metabolism of wheat, Triticum aestivum, var. Solstice. LPE allowed the measurement of benzoxazinoids, i.e. 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA), 2-hydroxy-7-methoxy-1,4-benzoxazin-3-one (HMBOA) and 6-methoxy-benzoxazolin-2-one (MBOA), and phenolic acids such as trans-p-coumaric acid, syringic acid, p-hydroxybenzoic acid, vanillic acid and cis- and trans-ferulic acid. Using LPE, a significantly higher level of DIMBOA was found in aerial parts and roots of T. aestivum following treatment with cis-jasmone, when compared with untreated plants. Similar results were obtained for phenolic acids, such as trans-ferulic acid and vanillic acid in roots. Using VPE, it was possible to measure levels of 2-hydroxy-7-methoxy-(2H)-1,4-benzoxazin-3(4H)-one (HBOA), benzoxazolin-2(3H)-one (BOA), ferulic acid, syringic acid and coumaric acid. The levels of HBOA in aerial parts and roots were significantly greater in cis-jasmone treated plants compared to untreated plants. cis-Jasmone is known to be a plant activator in terms of production of defence-related volatile semiochemicals that repel aphids and increase the foraging activity of aphid parasitoids. These results show, for the first time, that cis-jasmone also induces selective production of secondary metabolites that are capable of directly reducing development of pests, diseases and weeds.

The diverse and pervasive chemistries of the alpha-keto acid dependent enzymes

The number of identified and confirmed alpha-keto acid dependent oxygenases is increasing rapidly. All of these enzymes have a relatively simple liganding arrangement for a single ferrous ion but collectively conduct a highly diverse set of chemistries. While hydroxylations and a variety of oxidation reactions have been most commonly observed, new reactions involving dealkylations, epimerizations and halogenations have recently been discovered. In this minireview we present what is known of the alpha-keto acid dependent enzymes and offer an argument that the chemistry that is unique to each enzyme occurs only after the production of a pivotal ferryl-oxo intermediate.

Allelopathy in crop/weed interactions--an update

Since varietal differences in allelopathy of crops against weeds were discovered in the 1970s, much research has documented the potential that allelopathic crops offer for integrated weed management with substantially reduced herbicide rates. Research groups worldwide have identified several crop species possessing potent allelopathic interference mediated by root exudation of allelochemicals. Rice, wheat, barley and sorghum have attracted most attention. Past research focused on germplasm screening for elite allelopathic cultivars and the identification of the allelochemicals involved. Based on this, traditional breeding efforts were initiated in rice and wheat to breed agronomically acceptable, weed-suppressive cultivars with improved allelopathic interference. Promising suppressive crosses are under investigation. Molecular approaches have elucidated the genetics of allelopathy by QTL mapping which associated the trait in rice and wheat with several chromosomes and suggested the involvement of several allelochemicals. Potentially important compounds that are constitutively secreted from roots have been identified in all crop species under investigation. Biosynthesis and exudation of these metabolites follow a distinct temporal pattern and can be induced by biotic and abiotic factors. The current state of knowledge suggests that allelopathy involves fluctuating mixtures of allelochemicals and their metabolites as regulated by genotype and developmental stage of the producing plant, environment, cultivation and signalling effects, as well as the chemical or microbial turnover of compounds in the rhizosphere. Functional genomics is being applied to identify genes involved in biosynthesis of several identified allelochemicals, providing the potential to improve allelopathy by molecular breeding. The dynamics of crop allelopathy, inducible processes and plant signalling is gaining growing attention; however, future research should also consider allelochemical release mechanisms, persistence, selectivity and modes of action, as well as consequences of improved crop allelopathy on plant physiology, the environment and management strategies. Creation of weed-suppressive cultivars with improved allelopathic interference is still a challenge, but traditional breeding or biotechnology should pave the way.

Molecular cloning and functional characterization of psoralen synthase, the first committed monooxygenase of furanocoumarin biosynthesis

Ammi majus L. accumulates linear furanocoumarins by cytochrome P450 (CYP)-dependent conversion of 6-prenylumbelliferone via (+)-marmesin to psoralen. Relevant activities, i.e. psoralen synthase, are induced rapidly from negligible background levels upon elicitation of A. majus cultures with transient maxima at 9-10 h and were recovered in labile microsomes. Expressed sequence tags were cloned from elicited Ammi cells by a nested DD-RT-PCR strategy with CYP-specific primers, and full-size cDNAs were generated from those fragments correlated in abundance with the induction profile of furanocoumarin-specific activities. One of these cDNAs representing a transcript of maximal abundance at 4 h of elicitation was assigned CYP71AJ1. Functional expression in Escherichia coli or yeast cells initially failed but was accomplished eventually in yeast cells after swapping the N-terminal membrane anchor domain with that of CYP73A1. The recombinant enzyme was identified as psoralen synthase with narrow substrate specificity for (+)-marmesin. Psoralen synthase catalyzes a unique carbon-chain cleavage reaction concomitantly releasing acetone by syn-elimination. Related plants, i.e. Heracleum mantegazzianum, are known to produce both linear and angular furanocoumarins by analogous conversion of 8-prenylumbelliferone via (+)-columbianetin to angelicin, and it was suggested that angelicin synthase has evolved from psoralen synthase. However, (+)-columbianetin failed as substrate but competitively inhibited psoralen synthase activity. Analogy modeling and docked solutions defined the conditions for high affinity substrate binding and predicted the minimal requirements to accommodate (+)-columbianetin in the active site cavity. The studies suggested that several point mutations are necessary to pave the road toward angelicin synthase evolution.

Fate of benzoxazinone allelochemicals in soil after incorporation of wheat and rye sprouts

Growing cereals (especially rye), which are incorporated into the soil to increase soil fertility or organic matter content, is a common practice in crop rotation. The additional sanitizing effect of this incorporation has often been appreciated and is said to be due to leaching of benzoxazinones and subsequent formation of benzoxazolinones. In this study wheat (Stakado) and rye (Hacada) sprouts were incorporated into soil in amounts that simulated agricultural practice. By extraction and subsequent LC-MS analysis the disappearance and appearance of benzoxazinones, benzoxazolinones, and phenoxazinones in soil were followed. In the wheat experiments 6-methoxybenzoxazolin-2-one (MBOA) was detected as the main compound. 2-Hydroxy-7-methoxy-1,4-benzoxazin-3-one (HMBOA) and 2-hydroxy-1,4-benzoxazin-3-one (HBOA) were detected as well. No phenoxazinones were detected. For the rye experiment the picture was more complex. In the first 2 days of incubation MBOA and 2,4-dihydroxy-1,4-benzoxazin-3-one (DIBOA) were detected as the main allelochemicals along with HBOA, HMBOA, and benzoxazolin-2-one (BOA), in decreasing order. Later in the incubation period some 2-amino-3H-phenoxazin-3-one (APO) was detected and the amount of HBOA increased considerably and decreased again. The profiling of the benzoxazinone metabolites and their derivates in soil was dynamic and time-dependent. The highest concentrations of most of the compounds were seen at day 1 after incorporation. A maximum concentration was reached at day 4 for a few of the compounds. This study is the first of its kind that shows the dynamic pattern of biologically active benzoxazinone derivates in soil after incorporation of wheat and rye sprouts. Methods for organic synthesis of HBOA and HMBOA were developed as part of the study.

Three genomes differentially contribute to the biosynthesis of benzoxazinones in hexaploid wheat

Hexaploid wheat (Triticum aestivum) accumulates benzoxazinones (Bxs) as defensive compounds. Previously, we found that five Bx biosynthetic genes, TaBx1-TaBx5, are located on each of the three genomes (A, B, and D) of hexaploid wheat. In this study, we isolated three homoeologous cDNAs of each TaBx gene to estimate the contribution of individual homoeologous TaBx genes to the biosynthesis of Bxs in hexaploid wheat. We analyzed their transcript levels by homoeolog- or genome-specific quantitative RT-PCR and the catalytic properties of their translation products by kinetic analyses using recombinant TaBX enzymes. The three homoeologs were transcribed differentially, and the ratio of the individual homoeologous transcripts to total homoeologous transcripts also varied with the tissue, i.e., shoots or roots, as well as with the developmental stage. Moreover, the translation products of the three homoeologs had different catalytic properties. Some TaBx homoeologs were efficiently transcribed, but the translation products showed only weak enzymatic activities, which inferred their weak contribution to Bx biosynthesis. Considering the transcript levels and the catalytic properties collectively, we concluded that the homoeologs on the B genome generally contributed the most to the Bx biosynthesis in hexaploid wheat, especially in shoots. In tetraploid wheat and the three diploid progenitors of hexaploid wheat, the respective transcript levels of the TaBx homoeologs were similar in ratio to those observed in hexaploid wheat. This result indicates that the genomic bias in the transcription of the TaBx genes in hexaploid wheat originated in the diploid progenitors and has been retained through the polyploidization.

Seeing double: gene duplication and diversification in plant secondary metabolism

Gene duplications drive the recruitment of genes for secondary metabolism. Gene copies are gradually modified to create genes with specificities and expression patterns adapted to the needs of the new pathway in which they are involved. Duplicated genes are often in tandem repeats, forming clusters within the plant genome. However, in some cases, clusters of nonhomologous genes have also been identified as forming a functional unit. The selective forces that have caused the establishment of new pathways are far from understood and might have changed repeatedly during evolution owing to the continuously changing environment. Recent data show that the way several classes of secondary compounds are scattered among species is attributable to independent recruitment and the inactivation of biosynthetic enzymes.

Hydrogen peroxide-induced cell death in Arabidopsis: transcriptional and mutant analysis reveals a role of an oxoglutarate-dependent dioxygenase gene in the cell death process

Hydrogen peroxide is a major regulator of plant programmed cell death (PCD) but little is known about the downstream genes from the H(2)O(2)-signaling network that mediate the cell death. To address this question, a novel system for studying H(2)O(2)-induced programmed cell death in Arabidopsis thaliana was used. The catalase inhibitor aminotriazole (AT) reduced the catalase activity and caused endogenous accumulation of hydrogen peroxide that eventually triggered cell death. Microarray analysis with a DNA chip representing 21500 genes and subsequent comparison with other PCD-related expression studies revealed a set of new H(2)O(2)-responsive genes that were highly regulated in a common fashion during different types of PCD. These included an oxoglutarate-dependent dioxygenase and various oxidoreductases, the transcription factors Zat11, WRKY75 and NAM, proteasomal components, a heterologous group of genes with diverse functions, and genes encoding proteins with unknown functions. Knockout lines of the oxoglutarate-dependent dioxygenase exhibited significantly reduced death symptoms and chlorophyll loss upon H(2)O(2)-induced cell death, indicating a role for this gene in the cell death network.