Molecular Basis of the Evolution of Methylthioalkylmalate Synthase and the Diversity of Methionine-Derived Glucosinolates

Growth conditions trigger genotype-specific metabolic responses that affect the nutritional quality of kale cultivars

Kales (Brassica oleracea convar. acephala) are fast-growing, nutritious leafy vegetables ideal for year-round indoor farming. However, selection of the best cultivars for growth under artificial lighting necessitates a deeper understanding of leaf metabolism in different kale types. Here we examined a curly-leaved cultivar, Half Tall, and a lacinato-type cultivar, Black Magic, under moderate light (130 µmol photons m-2 s-1/22 °C) and high light (800 µmol photons m-2 s-1/26 °C) conditions. These conditions induced genotype-dependent differences in nutritionally important metabolites, especially anthocyanins and glucosinolates (GSLs), in kale cultivars. In the pale green Half Tall, growth under high light conditions did not induce changes in either pigmentation or total GSL content. In contrast, the purple pigmentation of Black Magic intensified due to increased anthocyanin accumulation. Black Magic showed reduced contents of indole GSLs and increased contents of aliphatic GSLs under high light conditions, with notable cultivar-specific adjustments in individual GSL species. Correlation analysis of metabolite profiles suggested cultivar-specific metabolic interplay between serine biosynthesis and the production of indole GSLs. RNA sequencing identified candidate genes encoding metabolic enzymes and regulatory components behind anthocyanin and GSL biosynthesis. These findings improve our understanding of leaf metabolism and its effects on the nutritional quality of kale cultivars.

Isopropylmalate synthase regulatory domain removal abolishes feedback regulation at the expense of leucine homeostasis in plants

In the leucine (Leu) biosynthesis pathway, homeostasis is achieved through a feedback regulatory mechanism facilitated by the binding of the end product Leu at the C-terminal regulatory domain of the first committed enzyme, isopropylmalate synthase (IPMS). In vitro studies have shown that removing the regulatory domain abolishes the feedback regulation on plant IPMS while retaining its catalytic activity. However, the physiological consequences and underlying molecular regulation of Leu flux upon removing the IPMS regulatory domain remain to be explored in plants. Here, we removed the IPMS C-terminal regulatory domain using a CRISPR/Cas9-based gene editing system and studied the resulting impact on the Leu biosynthesis pathway under in planta conditions. Absence of the IPMS regulatory domain unexpectedly reduced the formation of the end product Leu but increased the levels of Leu pathway intermediates in mustard (Brassica juncea). Additionally, delayed growth was observed when IPMS devoid of the regulatory domain was introduced into IPMS-null mutants of Escherichia coli and Arabidopsis thaliana. Further, a detailed biochemical analysis showed that in the absence of the C-terminal regulatory domain, a Leu pathway intermediate (α-ketoisocaproate) could compete with the native IPMS substrate (2-oxoisovalerate) for the active site. Combining these metabolomic, biochemical, and in planta analyses, we demonstrate that the C-terminal regulatory domain of IPMS is critical for maintaining Leu-Val homeostasis in plants.

Kinetic and catalytic mechanisms of the methionine-derived glucosinolate biosynthesis enzyme methylthioalkylmalate synthase

In Brassica plants, methionine-derived aliphatic glucosinolates are chemically diverse natural products that serve as plant defense compounds, as well as molecules with dietary health-promoting effects. During their biosynthesis, methylthioalkylmalate synthase (MAMS) catalyzes the elongation reaction of the aliphatic chain. The MAMS-catalyzed condensation of 4-methylthio-2-oxobutanoic acid and acetyl-CoA generates a 2-malate derivative that either enters the pathway for the synthesis of C3-glucosinolates or undergoes additional extension reactions, which lead to C4- to C9-glucosinolates. Recent determination of the x-ray crystal structure of MAMS from Brassica juncea (Indian mustard) provided insight on the molecular evolution of MAMS, especially substrate specificity changes, from the leucine biosynthesis enzyme α-isopropylmalate synthase but left details of the reaction mechanism unanswered. Here we use the B. juncea MAMS2A (BjMAMS2A) isoform to analyze the kinetic and catalytic mechanisms of this enzyme. Initial velocity studies indicate that MAMS follows an ordered bi bi kinetic mechanism, which based on the x-ray crystal structure, involves binding of 4-methylthio-2-oxobutanoic acid followed by acetyl-CoA. Examination of the pH-dependence of kcat and kcat/Km are consistent with acid/base catalysis. Site-directed mutagenesis of three residues originally proposed to function in the reaction mechanism-Arg89 (R89A, R89K, R89Q), Glu227 (E227A, E227D, E227Q), and His388 (H388A, H388N, H388Q, H388D, and H388E)-showed that only two mutants (E227Q and H388N) retained activity. Based on available structural and biochemical data, a revised reaction mechanism for MAMS-catalyzed elongation of methionine-derived aliphatic glucosinolates is proposed, which is likely also conserved in α-isopropylmalate synthase from leucine biosynthesis in plants and microbes.

4-Aldrithiol-based photometric assay for detection of methylthioalkylmalate synthase activity

In Brassica plants, glucosinolates are a diverse class of natural products, of which aliphatic methionine-derived glucosinolates are the most abundant form. Their structural diversity comes from the elongation of some side-chains by up to 9 carbons, which, after the formation of the core glucosinolate structure, can undergo further chemical modifications. Methylthioalkylmalate synthase (MAMS) catalyzes the iterative elongation process for aliphatic methionine-derived glucosinolates. Most biochemical studies on MAMS have been performed using liquid chromatography/mass spectrometry (LC/MS)-based assays or high-performance liquid chromatography (HPLC)-based assays. The LC/MS- and HPLC-based methods are endpoint assays, which cannot be monitored in real time and require a laborious process for data collection. These analytical methods are inefficient for performing multiple enzymatic assays needed to determine steady-state kinetic parameters or for mechanistic evaluation of pH-dependence and kinetic isotope effect studies. Although the function of MAMS has long been defined, there is a gap in knowledge as it pertains to biochemical characterization of this plant enzyme. Part of this may be due to the lack of efficient methods that can be used for this type of research. This chapter describes a continuous photometric assay to track MAMS activity in real time using the 4-aldrithiol reagent for reaction detection.

Characterization of unique EDTA-insensitive methylthioalkylmalate synthase from Eutrema japonicum and its potential application in synthetic biology

6-(Methylsulfinyl)hexyl isothiocyanate (6-MSITC), a derivative of glucosinolate with a six-carbon chain, is a compound found in wasabi and has diverse health-promoting properties. The biosynthesis of glucosinolates from methionine depends on a crucial step catalyzed methylthioalkylmalate synthases (MAMs), which are responsible for the generation of glucosinolates with varying chain lengths. In this study, our primary focus was the characterization of two methylthioalkyl malate synthases, MAM1-1 and MAM1-2, derived from Eutrema japonicum, commonly referred to as Japanese wasabi. Eutremajaponicum MAMs (EjMAMs) were expressed in an Escherichiacoli expression system, subsequently purified, and in vitro enzymatic activity was assayed. We explored the kinetic properties, optimal pH conditions, and cofactor preferences of EjMAMs and compared them with those of previously documented MAMs. Surprisingly, EjMAM1-2, categorized as a metallolyase family enzyme, displayed 20% of its maximum activity even in the absence of divalent metal cofactors or under high concentrations of EDTA. Additionally, we utilized AlphaFold2 to generate structural homology models of EjMAMs, and used in silico analysis and mutagenesis studies to investigate the key residues participating in catalytic activity. Moreover, we examined in vivo biosynthesis in E. coli containing Arabidopsis thaliana branched-chain amino acid transferase 3 (AtBCAT3) along with AtMAMs or EjMAMs and demonstrated that EjMAM1-2 exhibited the highest conversion rate among those MAMs, converting l-methionine to 2-(2-methylthio) ethyl malate (2-(2-MT)EM). EjMAM1-2 shows a unique property in vitro and highest activity on converting l-methionine to 2-(2-MT)EM in vivo which displays high potential for isothiocyanate biosynthesis in E. coli platform.

Functional and regulatory diversity of homeobox-leucine zipper transcription factors BnaHB6 under dehydration and salt stress in Brassica napus L

The plant-specific homeodomain-leucine zipper I subfamily is involved in the regulation of various biological processes, particularly growth, development and stress response. In the present study, we characterized four BnaHB6 homologues from Brassica napus. All BnaHB6 proteins have transcriptional activation activity. Structural and functional data indicate the complex role of BnaHB6 genes in regulating biological processes, with some functions conserved and others diverged. Transcriptional analyzes revealed that they are induced in a similar manner in different tissues but show different expression patterns in response to stress and circadian rhythm. Only the BnaA09HB6 and BnaC08HB6 genes are expressed under dehydration and salt stress, and in darkness. The partial transcriptional overlap of BnaHB6s with the evolutionarily related genes BnaHB5 and BnaHB16 was also observed. Transgenic Arabidopsis thaliana plants expressing a single proBnaHB6::GUS partially confirmed the expression results. Bioinformatic analysis allowed the identification of TF-binding sites in the BnaHB6 promoters that may control their expression under stress and circadian rhythm. ChIP-qPCR analysis revealed that BnaA09HB6 and BnaC08HB6 bind directly to the promoters of the target genes BnaABF4 and BnaDREB2A. Comparison of their expression patterns in the WT plants and the bnac08hb6 mutant showed that BnaC08HB6 positively regulates the expression of the BnaABF4 and BnaDREB2A genes under dehydration and salt stress. We conclude that four BnaHB6 homologues have distinct functions in response to stress despite high sequence similarity, possibly indicating different binding preferences with BnaABF4 and BnaDREB2A. We hypothesize that BnaC08HB6 and BnaA09HB6 function in a complex regulatory network under stress.

Chromosome-scale reference genome of broccoli (Brassica oleracea var. italica Plenck) provides insights into glucosinolate biosynthesis

Broccoli (Brassica oleracea var. italica Plenck) is an important vegetable crop, as it is rich in health-beneficial glucosinolates (GSLs). However, the genetic basis of the GSL diversity in Brassicaceae remains unclear. Here we report a chromosome-level genome assembly of broccoli generated using PacBio HiFi reads and Hi-C technology. The final genome assembly is 613.79 Mb in size, with a contig N50 of 14.70 Mb. The GSL profile and content analysis of different B. oleracea varieties, combined with a phylogenetic tree analysis, sequence alignment, and the construction of a 3D model of the methylthioalkylmalate synthase 1 (MAM1) protein, revealed that the gene copy number and amino acid sequence variation both contributed to the diversity of GSL biosynthesis in B. oleracea. The overexpression of BoMAM1 (BolI0108790) in broccoli resulted in high accumulation and a high ratio of C4-GSLs, demonstrating that BoMAM1 is the key enzyme in C4-GSL biosynthesis. These results provide valuable insights for future genetic studies and nutritive component applications of Brassica crops.

Complementing model species with model clades

Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade." These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales.

Developing multifunctional crops by engineering Brassicaceae glucosinolate pathways

Glucosinolates (GSLs), found mainly in species of the Brassicaceae family, are one of the most well-studied classes of secondary metabolites. Produced by the action of myrosinase on GSLs, GSL-derived hydrolysis products (GHPs) primarily defend against biotic stress in planta. They also significantly affect the quality of crop products, with a subset of GHPs contributing unique food flavors and multiple therapeutic benefits or causing disagreeable food odors and health risks. Here, we explore the potential of these bioactive functions, which could be exploited for future sustainable agriculture. We first summarize our accumulated understanding of GSL diversity and distribution across representative Brassicaceae species. We then systematically discuss and evaluate the potential of exploited and unutilized genes involved in GSL biosynthesis, transport, and hydrolysis as candidate GSL engineering targets. Benefiting from available information on GSL and GHP functions, we explore options for multifunctional Brassicaceae crop ideotypes to meet future demand for food diversification and sustainable crop production. An integrated roadmap is subsequently proposed to guide ideotype development, in which maximization of beneficial effects and minimization of detrimental effects of GHPs could be combined and associated with various end uses. Based on several use-case examples, we discuss advantages and limitations of available biotechnological approaches that may contribute to effective deployment and could provide novel insights for optimization of future GSL engineering.

Genetic Improvement of Camelina sativa (L.) Crantz: Opportunities and Challenges

In recent years, a renewed interest in novel crops has been developing due to the environmental issues associated with the sustainability of agricultural practices. In particular, a cover crop, Camelina sativa (L.) Crantz, belonging to the Brassicaceae family, is attracting the scientific community's interest for several desirable features. It is related to the model species Arabidopsis thaliana, and its oil extracted from the seeds can be used either for food and feed, or for industrial uses such as biofuel production. From an agronomic point of view, it can grow in marginal lands with little or no inputs, and is practically resistant to the most important pathogens of Brassicaceae. Although cultivated in the past, particularly in northern Europe and Italy, in the last century, it was abandoned. For this reason, little breeding work has been conducted to improve this plant, also because of the low genetic variability present in this hexaploid species. In this review, we summarize the main works on this crop, focused on genetic improvement with three main objectives: yield, seed oil content and quality, and reduction in glucosinolates content in the seed, which are the main anti-nutritional substances present in camelina. We also report the latest advances in utilising classical plant breeding, transgenic approaches, and CRISPR-Cas9 genome-editing.

Synthesis of 4-methylvaleric acid, a precursor of pogostone, involves a 2-isobutylmalate synthase related to 2-isopropylmalate synthase of leucine biosynthesis

We show here that the side chain of pogostone, one of the major components of patchouli oil obtained from Pogostemon cablin and possessing a variety of pharmacological activities, is derived from 4-methylvaleric acid. We also show that 4-methylvaleric acid is produced through the one-carbon α-ketoacid elongation pathway with the involvement of the key enzyme 2-isobutylmalate synthase (IBMS), a newly identified enzyme related to isopropylmalate synthase (IPMS) of leucine (Leu) biosynthesis. Site-directed mutagenesis identified Met¹³² in the N-terminal catalytic region as affecting the substrate specificity of PcIBMS1. Even though PcIBMS1 possesses the C-terminal domain that in IPMS serves to mediate Leu inhibition, it is insensitive to Leu. The observation of the evolution of IBMS from IPMS, as well as previously reported examples of IPMS-related genes involved in making glucosinolates in Brassicaceae, acylsugars in Solanaceae, and flavour compounds in apple, indicate that IPMS genes represent an important pool for the independent evolution of genes for specialised metabolism.

Deep roots and many branches: Origins of plant-specialized metabolic enzymes in general metabolism

Collectively, plants produce hundreds of thousands of specialized metabolites from simple building blocks such as amino acids, fatty acids, and isoprenoids. As additional specialized metabolic enzymes are described, there is increasing recognition of the importance of cooption of general metabolic enzymes to specialized metabolism by gene duplication, narrowing of expression, and alteration of enzymatic activities. Here, we examine how several classes of enzymes were each coopted multiple times. We demonstrate the simplicity of achieving the synthesis of analogous chemicals by coopting existing enzymes and summarize emerging insights that could inform rational metabolic engineering of both general and specialized metabolic enzymes.

Ancient Biosyntheses in an Oil Crop: Glucosinolate Profiles in Limnanthes alba and Its Relatives (Limnanthaceae, Brassicales)

The glucosinolate (GSL) profiles of four Limnanthaceae species, including the oil crop Limnanthes alba (meadowfoam), were investigated by an ultrahigh-performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry (UHPLC-QToF-MS/MS) analysis of desulfoGSLs after desulfation of native GSLs, supplemented by NMR of desulfated 2-hydroxy-2-methylpropylGSL and 3-methoxybenzylGSL. Leaves, roots, and seeds were investigated, providing an overview of biosynthetic capabilities in the genera Floerkea and Limnanthes. Methoxyl groups on benzylGSLs were in meta but not para positions; two 3,5-disubstituted benzylGSLs are tentatively proposed. 2-Hydroxy-2-methylpropylGSL was accompanied by an isomer that was not a previously reported GSL. The combined GSL profile of the family included GSLs derived from valine, leucine, isoleucine, phenylalanine, and tyrosine, and possibly methionine and tryptophan. Substituted indole GSLs and GSLs derived from chain-elongated amino acids or alanine were searched for but not detected. Hypothetic glycosides of GSLs were detected at low levels. Based on biochemical interpretation, we suggest biosynthetic schemes and gene families (CYP79C, GSOH) relevant for tailoring GSL profiles in Limnanthes crops.

Glucosinolate biosynthesis: role of MAM synthase and its perspectives

Glucosinolates, synthesized by the glucosinolate biosynthesis pathway, are the secondary metabolites used as a defence mechanism in the Brassicaceae plants, including Arabidopsis thaliana. The first committed step in the pathway, catalysed by methylthioalkylmalate (MAM) synthase (EC: 2.3.3.17), is to produce different variants of glucosinolates. Phylogenetic analyses suggest that possibly MAM synthases have been evolved from isopropylmalate synthase (IPMS) by the substitutions of five amino acid residues (L143I, H167L, S216G, N250G and P252G) in the active site of IPMS due to point mutations. Considering the importance of MAM synthase in Brassicaceae plants, Petersen et al. (2019) made an effort to characterise the MAM synthase (15 MAM1 variants) in vitro by single substitution or double substitutions. In their study, the authors have expressed the variants in Escherichia coli and analysed the amino acids in the cultures of E. coli in vivo. Since modifying the MAM synthases by transgenic approaches could increase the resistance of Brassicaceae plants for enhancing the defence effect of glucosinolates and their degraded products; hence, MAM synthases should be characterized in detail in vivo in A. thaliana along with the structural analysis of the enzyme for meaningful impact and for its imminent use in vivo.

Structural Studies of Aliphatic Glucosinolate Chain-Elongation Enzymes

Plants evolved specialized metabolic pathways through gene duplication and functional divergence of enzymes involved in primary metabolism. The results of this process are varied pathways that produce an array of natural products useful to both plants and humans. In plants, glucosinolates are a diverse class of natural products. Glucosinolate function stems from their hydrolysis products, which are responsible for the strong flavors of Brassicales plants, such as mustard, and serve as plant defense molecules by repelling insects, fighting fungal infections, and discouraging herbivory. Additionally, certain hydrolysis products such as isothiocyanates can potentially serve as cancer prevention agents in humans. The breadth of glucosinolate function is a result of its great structural diversity, which comes from the use of aliphatic, aromatic and indole amino acids as precursors and elongation of some side chains by up to nine carbons, which, after the formation of the core glucosinolate structure, can undergo further chemical modifications. Aliphatic methionine-derived glucosinolates are the most abundant form of these compounds. Although both elongation and chemical modification of amino acid side chains are important for aliphatic glucosinolate diversity, its elongation process has not been well described at the molecular level. Here, we summarize new insights on the iterative chain-elongation enzymes methylthioalkylmalate synthase (MAMS) and isopropylmalate dehydrogenase (IPMDH).

Improvement of glucosinolates by metabolic engineering in Brassica crops

Glucosinolates (GSLs) are a class of sulfur- and nitrogen-containing, and amino acid-derived important secondary metabolites, which mainly present in plants of Brassicaceae family, including Brassica crops, such as broccoli, cabbage, and oilseed rape. The bioactive GSL metabolites confer benefits to plant defense, human health, and the unique flavor of some Brassica crops. However, certain GSL profiles have adverse effects and are known as anti-nutritional factors. This has attracted mounting attempts to increase beneficial GSLs and reduce detrimental ones in the most commonly consumed Brassica crops. We provide a comprehensive overview of metabolic engineering applied in Brassica crops to achieve this purpose, including modulation of GSL biosynthesis, ablation of GSL hydrolysis, inhibition of GSL transport processes, and redirection of metabolic flux to GSL. Moreover, advances in omics approaches, i.e., genomics, transcriptome, and metabolome, applied in the elucidation of GSL metabolism in Brassica crops, as well as promising and potential genome-editing technologies are also discussed.

A complex interplay of Gβ and Gγ proteins regulates plant growth and defence traits in the allotetraploid Brassica juncea

Gene expression analysis coupled with in-planta studies showed that specific Gβγ combination regulates plant growth and defence traits in the allotetraploid Brassica juncea. Plant heterotrimeric G-proteins regulate a wide range of responses despite their limited repertoire of core components. The roles and functional interactions between different G-protein subunits are quite perplexing, which get further complicated with polyploidy. Here, we show that the allotetraploid Brassica juncea comprises multiple homologs of G-protein genes, encoding six BjuGβ and ten highly divergent BjuGγ subunit proteins, later being classified into type-A1, type-A2 and type-C Gγ proteins. The encoded BjuGβ and BjuGγ proteins shared close evolutionary relationship and have retained distinct spatio-temporal expression patterns during plant developmental stages and in response to the necrotrophic pathogen, Sclerotinia sclerotiorum. RNAi based suppression of BjuGβ and BjuGγ genes suggested functional overlap and selectivity of BjuGβs with three distinct BjuGγ type subunits, to regulate plant height (BjuGβγA2 and BjuGβγC), seed weight (BjuGβGγA1 and BjuGβGγC), silique size (BjuGβGγC) and pathogen response (BjuGβGγA1 and BjuGβGγC). Further, the triplicated BjuGβ genes, formed due to Brassica specific whole-genome-triplication event, showed differential involvement during pathogen response, wherein overexpression of BjuGβ2 displayed higher resistance to Sclerotinia infection. Taken together, our study demonstrates that multiple BjuGβ and BjuGγ proteins have retained distinct spatio-temporal expression and functional selectivity to regulate specific plant growth and defence traits in the oilseed B. juncea.

GTR1 and GTR2 transporters differentially regulate tissue-specific glucosinolate contents and defence responses in the oilseed crop Brassica juncea

GTR1 and GTR2 transporters are components of the source to sink translocation network of glucosinolates, which are major defence metabolites in the Brassicaceae. These transporters can be genetically manipulated for reduction of seed-glucosinolates without inhibiting glucosinolate biosynthesis, thereby maintaining the inherent defence potential of plants. However, the different roles of GTRs in influencing tissue-specific distribution of glucosinolates in agriculturally important Brassica crops are yet unknown. Here, we report functional characterization of two groups of glucosinolate transporters (GTR1 and GTR2) from Brassica juncea based on gene expression data, biochemical analysis, gene-complementation studies in GTR-deficient mutants and RNAi-based knockdown followed by insect feeding experiments. Although both GTRs showed ubiquitous expression patterns and broad substrate specificity, the single-gene knockdown lines displayed different phenotypes. The GTR2-knockdown plants showed a significant reduction of glucosinolates in seeds and a higher accumulation in leaves and pods, while the GTR1-knockdown plants displayed a smaller reduction of glucosinolates in seeds and significantly lower glucosinolate levels in leaves. Consequently, knockdown of GTR2 resulted in higher resistance towards the generalist pest, Spodoptera litura. Overall, our study highlights the distinctive roles of B. juncea GTRs in tissue-specific accumulation of glucosinolates and the potential for manipulating GTR2 for enhanced nutrition and plant defence.

Engineering and optimization of the 2-phenylethylglucosinolate production in Nicotiana benthamiana by combining biosynthetic genes from Barbarea vulgaris and Arabidopsis thaliana

2-Phenylethylglucosinolate (2PE) derived from homophenylalanine is present in plants of the Brassicales order as a defense compound. It is associated with multiple biological properties, including deterrent effects on pests and antimicrobial and health-promoting functions, due to its hydrolysis product 2-phenylethyl isothiocyanate, which confers 2PE as a potential application in agriculture and industry. In this study, we characterized the putative key genes for 2PE biosynthesis from Barbarea vulgaris W.T. Aiton and demonstrated the feasibility of engineering 2PE production in Nicotiana benthamiana Domin. We used different combinations of genes from B. vulgaris and Arabidopsis thaliana (L.) Heynh. to demonstrate that: (i) BvBCAT4 performed more efficiently than AtBCAT4 in biosynthesis of both homophenylalanine and dihomomethionine; (ii) MAM1 enzymes were critical for the chain-elongated profile, while CYP79F enzymes accepted both chain-elongated methionine and homophenylalanine; (iii) aliphatic but not aromatic core structure pathway catalyzed the 2PE biosynthesis; (iv) a chimeric pathway containing BvBCAT4, BvMAM1, AtIPMI and AtIPMDH1 resulted in a two-fold increase in 2PE production compared with the B. vulgaris-specific chain elongation pathway; and (v) profiles of chain-elongated products and glucosinolates partially mirrored the profiles in the gene donor plant, but were wider in N. benthamiana than in the native plants. Our study provides a strategy to produce the important homophenylalanine and 2PE in a heterologous host. Furthermore, chimeric engineering of the complex 2PE biosynthetic pathway enabled detailed understanding of catalytic properties of individual enzymes - a prerequisite for understanding biochemical evolution. The new-to-nature gene combinations have the potential for application in biotechnological and plant breeding.

Glucosinolate profiles and phylogeny in Barbarea compared to other tribe Cardamineae (Brassicaceae) and Reseda (Resedaceae), based on a library of ion trap HPLC-MS/MS data of reference desulfoglucosinolates

A library of ion trap MS2 spectra and HPLC retention times reported here allowed distinction in plants of at least 70 known glucosinolates (GSLs) and some additional proposed GSLs. We determined GSL profiles of selected members of the tribe Cardamineae (Brassicaceae) as well as Reseda (Resedaceae) used as outgroup in evolutionary studies. We included several accessions of each species and a range of organs, and paid attention to minor peaks and GSLs not detected. In this way, we obtained GSL profiles of Barbarea australis, Barbarea grayi, Planodes virginica selected for its apparent intermediacy between Barbarea and the remaining tribe and family, and Rorippa sylvestris and Nasturtium officinale, for which the presence of acyl derivatives of GSLs was previously untested. We also screened Armoracia rusticana, with a remarkably diverse GSL profile, the emerging model species Cardamine hirsuta, for which we discovered a GSL polymorphism, and Reseda luteola and Reseda odorata. The potential for aliphatic GSL biosynthesis in Barbarea vulgaris was of interest, and we subjected P-type and G-type B. vulgaris to several induction regimes in an attempt to induce aliphatic GSL. However, aliphatic GSLs were not detected in any of the B. vulgaris types. We characterized the investigated chemotypes phylogenetically, based on nuclear rDNA internal transcribed spacer (ITS) sequences, in order to understand their relation to the species B. vulgaris in general, and found them to be representative of the species as it occurs in Europe, as far as documented in available ITS-sequence repositories. In short, we provide GSL profiles of a wide variety of tribe Cardamineae plants and conclude aliphatic GSLs to be absent or below our limit of detection in two major evolutionary lines of B. vulgaris. Concerning analytical chemistry, we conclude that availability of authentic reference compounds or reference materials is critical for reliable GSL analysis and characterize two publicly available reference materials: seeds of P. virginica and N. officinale.

Comparison of glucosinolate diversity in the crucifer tribe Cardamineae and the remaining order Brassicales highlights repetitive evolutionary loss and gain of biosynthetic steps

We review glucosinolate (GSL) diversity and analyze phylogeny in the crucifer tribe Cardamineae as well as selected species from Brassicaceae (tribe Brassiceae) and Resedaceae. Some GSLs occur widely, while there is a scattered distribution of many less common GSLs, tentatively sorted into three classes: ancient, intermediate and more recently evolved. The number of conclusively identified GSLs in the tribe (53 GSLs) constitute 60% of all GSLs known with certainty from any plant (89 GSLs) and apparently unique GSLs in the tribe constitute 10 of those GSLs conclusively identified (19%). Intraspecific, qualitative GSL polymorphism is known from at least four species in the tribe. The most ancient GSL biosynthesis in Brassicales probably involved biosynthesis from Phe, Val, Leu, Ile and possibly Trp, and hydroxylation at the β-position. From a broad comparison of families in Brassicales and tribes in Brassicaceae, we estimate that a common ancestor of the tribe Cardamineae and the family Brassicaceae exhibited GSL biosynthesis from Phe, Val, Ile, Leu, possibly Tyr, Trp and homoPhe (ancient GSLs), as well as homologs of Met and possibly homoIle (intermediate age GSLs). From the comparison of phylogeny and GSL diversity, we also suggest that hydroxylation and subsequent methylation of indole GSLs and usual modifications of Met-derived GSLs (formation of sulfinyls, sulfonyls and alkenyls) occur due to conserved biochemical mechanisms and was present in a common ancestor of the family. Apparent loss of homologs of Met as biosynthetic precursors was deduced in the entire genus Barbarea and was frequent in Cardamine (e.g. C. pratensis, C. diphylla, C. concatenata, possibly C. amara). The loss was often associated with appearance of significant levels of unique or rare GSLs as well as recapitulation of ancient types of GSLs. Biosynthetic traits interpreted as de novo evolution included hydroxylation at rare positions, acylation at the thioglucose and use of dihomoIle and possibly homoIle as biosynthetic precursors. Biochemical aspects of the deduced evolution are discussed and testable hypotheses proposed. Biosyntheses from Val, Leu, Ile, Phe, Trp, homoPhe and homologs of Met are increasingly well understood, while GSL biosynthesis from mono- and dihomoIle is poorly understood. Overall, interpretation of known diversity suggests that evolution of GSL biosynthesis often seems to recapitulate ancient biosynthesis. In contrast, unprecedented GSL biosynthetic innovation seems to be rare.

A comprehensive Vis-NIRS equation for rapid quantification of seed glucosinolate content and composition across diverse Brassica oilseed chemotypes

The globally cultivated Brassica crops contain high deliverable concentrations of health-promoting glucosinolates. Development of a Visible-Near InfraRed Spectroscopy (Vis-NIRS) calibration to profile different glucosinolate components from 641 diverse Brassica juncea chemotypes was attempted in this study. Principal component analysis of HPLC-determined glucosinolates established the distinctiveness of four B. juncea populations used. Subsequently, modified partial least square regression based population-specific and combined Vis-NIRS models were developed, wherein the combined model exhibited higher coefficient of determination (R²; 0.81-0.97) for eight glucosinolates and higher ratio of prediction determination (RPD; 2.42-5.35) for seven glucosinolates in B. juncea populations. Furthermore, range error ratio (RER > 4) for twelve and RER > 10 for eight glucosinolates make the combined model acceptable for screening and quality control. The model also provided excellent prediction for aliphatic glucosinolates in four oilseed Brassica species. Overall, our work highlights the potential of Vis-NIR spectroscopy in estimating glucosinolate content in the economically important Brassica oilseeds.

Site-directed mutagenesis identified the key active site residues of alcohol acyltransferase PpAAT1 responsible for aroma biosynthesis in peach fruits

The aroma of peach fruit is predominantly determined by the accumulation of γ-decalactone and ester compounds. A previous study showed that the biosynthesis of these aroma compounds in peach fruit is catalyzed by PpAAT1, an alcohol acyltransferase. In this work, we investigated the key active site residues responsible for γ-decalactone and ester biosynthesis. A total of 14 candidate amino acid residues possibly involved in internal esterification and 9 candidate amino acid residues possibly involved in esterification of PpAAT1 were assessed via site-directed mutagenesis. Analyses of the in vitro enzyme activities of PpAAT1 and its site-directed mutant proteins (PpAAT1-SMs) with different amino acid residue mutations as well as the contents of γ-decalactone in transgenic tobacco leaves and peach fruits transiently expressing PpAAT1 and PpAAT1-SMs revealed that site-directed mutation of H165 in the conserved HxxxD motif led to lost enzymatic activity of PpAAT1 in both internal esterification and its reactions, whereas mutation of the key amino acid residue D376 led to the total loss of γ-decalactone biosynthesis activity of PpAAT1. Mutations of 9 and 7 other amino acid residues also dramatically affected the enzymatic activity of PpAAT1 in the internal esterification and esterification reactions, respectively. Our findings provide a biochemical foundation for the mechanical biosynthesis of γ-decalactone and ester compounds catalyzed by PpAAT1 in peach fruits, which could be used to guide the molecular breeding of new peach species with more favorable aromas for consumers.

Citramalate synthase yields a biosynthetic pathway for isoleucine and straight- and branched-chain ester formation in ripening apple fruit

A plant pathway that initiates with the formation of citramalate from pyruvate and acetyl-CoA by citramalate synthase (CMS) is shown to contribute to the synthesis of α-ketoacids and important odor-active esters in apple (Malus × domestica) fruit. Microarray screening led to the discovery of a gene with high amino acid similarity to 2-isopropylmalate synthase (IPMS). However, functional analysis of recombinant protein revealed its substrate preference differed substantially from IPMS and was more typical of CMS. MdCMS also lacked the regulatory region present in MdIPMS and was not sensitive to feedback inhibition. 13C-acetate feeding of apple tissue labeled citramalate and α-ketoacids in a manner consistent with the presence of the citramalate pathway, labeling both straight- and branched-chain esters. Analysis of genomic DNA (gDNA) revealed the presence of two nearly identical alleles in "Jonagold" fruit (MdCMS_1 and MdCMS_2), differing by two nonsynonymous single-nucleotide polymorphisms (SNPs). The mature proteins differed only at amino acid 387, possessing either glutamine387 (MdCMS_1) or glutamate387 (MdCMS_2). Glutamate387 was associated with near complete loss of activity. MdCMS expression was fruit-specific, increasing severalfold during ripening. The translated protein product was detected in ripe fruit. Transient expression of MdCMS_1 in Nicotiana benthamiana induced the accumulation of high levels of citramalate, whereas MdCMS_2 did not. Domesticated apple lines with MdCMS isozymes containing only glutamate387 produced a very low proportion of 2-methylbutanol- and 2-methylbutanoate (2MB) and 1-propanol and propanoate (PROP) esters. The citramalate pathway, previously only described in microorganisms, is shown to function in ripening apple and contribute to isoleucine and 2MB and PROP ester biosynthesis without feedback regulation.

Glucosinolate Biosynthesis and the Glucosinolate–Myrosinase System in Plant Defense

Insect pests represent a major global challenge to important agricultural crops. Insecticides are often applied to combat such pests, but their use has caused additional challenges such as environmental contamination and human health issues. Over millions of years, plants have evolved natural defense mechanisms to overcome insect pests and pathogens. One such mechanism is the production of natural repellents or specialized metabolites like glucosinolates. There are three types of glucosinolates produced in the order Brassicales: aliphatic, indole, and benzenic glucosinolates. Upon insect herbivory, a “mustard oil bomb” consisting of glucosinolates and their hydrolyzing enzymes (myrosinases) is triggered to release toxic degradation products that act as insect deterrents. This review aims to provide a comprehensive summary of glucosinolate biosynthesis, the “mustard oil bomb”, and how these metabolites function in plant defense against pathogens and insects. Understanding these defense mechanisms will not only allow us to harness the benefits of this group of natural metabolites for enhancing pest control in Brassicales crops but also to transfer the “mustard oil bomb” to non-glucosinolate producing crops to boost their defense and thereby reduce the use of chemical pesticides.

flasher, a novel mutation in a glucosinolate modifying enzyme, conditions changes in plant architecture and hormone homeostasis

Meristem function is underpinned by numerous genes that affect hormone levels, ultimately controlling phyllotaxy, the transition to flowering and general growth properties. Class I KNOX genes are major contributors to this process, promoting cytokinin biosynthesis but repressing gibberellin production to condition a replication competent state. We identified a suppressor mutant of the KNOX1 mutant brevipedicellus (bp) that we termed flasher (fsh), which promotes stem and pedicel elongation, suppresses early senescence, and negatively affects reproductive development. Map-based cloning and complementation tests revealed that fsh is due to an E40K change in the flavin monooxygenase GS-OX5, a gene encoding a glucosinolate (GSL) modifying enzyme. In vitro enzymatic assays revealed that fsh poorly converts substrate to product, yet the levels of several GSLs are higher in the suppressor line, implicating FSH in feedback control of GSL flux. FSH is expressed predominantly in the vasculature in patterns that do not significantly overlap those of BP, implying a non-cell autonomous mode of meristem control via one or more GSL metabolites. Hormone analyses revealed that cytokinin levels are low in bp, but fsh restores cytokinin levels to near normal by activating cytokinin biosynthesis genes. In addition, jasmonate levels in the fsh suppressor are significantly lower than in bp, which is likely due to elevated expression of JA inactivating genes. These observations suggest the involvement of the GSL pathway in generating one or more negative effectors of growth that influence inflorescence architecture and fecundity by altering the balance of hormonal regulators.

The evolution of metabolism: How to test evolutionary hypotheses at the genomic level

The origin of primordial metabolism and its expansion to form the metabolic networks extant today represent excellent systems to study the impact of natural selection and the potential adaptive role of novel compounds. Here we present the current hypotheses made on the origin of life and ancestral metabolism and present the theories and mechanisms by which the large chemical diversity of plants might have emerged along evolution. In particular, we provide a survey of statistical methods that can be used to detect signatures of selection at the gene and population level, and discuss potential and limits of these methods for investigating patterns of molecular adaptation in plant metabolism.

Genomic Origin and Diversification of the Glucosinolate MAM Locus

Glucosinolates are a diverse group of plant metabolites that characterize the order Brassicales. The MAM locus is one of the most significant QTLs for glucosinolate diversity. However, most of what we understand about evolution at the locus is focused on only a few species and not within a phylogenetic context. In this study, we utilize a micro-synteny network and phylogenetic inference to investigate the origin and diversification of the MAM/IPMS gene family. We uncover unique MAM-like genes found at the orthologous locus in the Cleomaceae that shed light on the transition from IPMS to MAM. In the Brassicaceae, we identify six distinct MAM clades across Lineages I, II, and III. We characterize the evolutionary impact and consequences of local duplications, transpositions, whole genome duplications, and gene fusion events, generating several new hypothesizes on the function and diversity of the MAM locus.

Location, location! cellular relocalization primes specialized metabolic diversification

Specialized metabolites are structurally diverse and cell- or tissue-specific molecules produced in restricted plant lineages. In contrast, primary metabolic pathways are highly conserved in plants and produce metabolites essential for all of life, such as amino acids and nucleotides. Substrate promiscuity - the capacity to accept non-native substrates - is a common characteristic of enzymes, and its impact is especially apparent in generating specialized metabolite variation. However, promiscuity only leads to metabolic diversity when alternative substrates are available; thus, enzyme cellular and subcellular localization directly influence chemical phenotypes. We review a variety of mechanisms that modulate substrate availability for promiscuous plant enzymes. We focus on examples where evolution led to modification of the 'cellular context' through changes in cell-type expression, subcellular relocalization, pathway sequestration, and cellular mixing via tissue damage. These varied mechanisms contributed to the emergence of structurally diverse plant specialized metabolites and inform future metabolic engineering approaches.