A reference genome for the long-term kleptoplast-retaining sea slug Elysia crispata morphotype clarki

Several species of sacoglossan sea slugs possess the incredible ability to sequester chloroplasts from the algae they consume. These "photosynthetic animals" incorporate stolen chloroplasts, called kleptoplasts, into the epithelial cells of tubules that extend from their digestive tracts throughout their bodies. The mechanism by which these slugs maintain functioning kleptoplasts in the absence of an algal nuclear genome is unknown. Here, we report a draft genome of the sacoglossan slug Elysia crispata morphotype clarki, a morphotype native to the Florida Keys that can retain photosynthetically active kleptoplasts for several months without feeding. We used a combination of Oxford Nanopore Technologies long reads and Illumina short reads to produce a 786-Mb assembly (N50 = 0.459 Mb) containing 68,514 predicted protein-coding genes. A phylogenetic analysis found no evidence of horizontal acquisition of genes from algae. We performed gene family and gene expression analyses to identify E. crispata genes unique to kleptoplast-containing slugs that were more highly expressed in fed versus unfed developmental life stages. Consistent with analyses in other kleptoplastic slugs, our investigation suggests that genes encoding lectin carbohydrate-binding proteins and those involved in regulation of reactive oxygen species and immunity may play a role in kleptoplast retention. Lastly, we identified four polyketide synthase genes that could potentially encode proteins producing UV- and oxidation-blocking compounds in slug cell membranes. The genome of E. crispata is a quality resource that provides potential targets for functional analyses and enables further investigation into the evolution and mechanisms of kleptoplasty in animals.

Strategies to study the metabolic origins of specialized plant metabolites: The specialized 1,4-naphthoquinones

One of the hallmarks of specialized plant metabolites is that they are produced using precursors from central metabolism. Therefore, in addition to identifying and characterizing the pathway genes and enzymes involved in synthesizing a specialized compound, it is critical to study its metabolic origins. Identifying what primary metabolic pathways supply precursors to specialized metabolism and how primary metabolism has diversified to sustain fluxes to specialized metabolite pathways is imperative to optimizing synthetic biology strategies for producing high-value plant natural products in crops and microbial systems. Improved understanding of the metabolic origins of specialized plant metabolites has also revealed instances of recurrent evolution of the same compound, or nearly identical compounds, with similar ecological functions, thereby expanding knowledge about the factors driving the chemical diversity in the plant kingdom. In this chapter, we describe detailed methods for performing tracer studies, chemical inhibitor experiments, and reverse genetics. We use examples from investigations of the metabolic origins of specialized plant 1,4-naphthoquinones (1,4-NQs). The plant 1,4-NQs provide an excellent case study for illustrating the importance of investigating the metabolic origins of specialized metabolites. Over half a century of research by many groups has revealed that the pathways to synthesize plant 1,4-NQs are the result of multiple events of convergent evolution across several disparate plant lineages and that plant 1,4-NQ pathways are supported by extraordinary events of metabolic innovation and by various primary metabolic sources.

Seedling growth and fall armyworm feeding preference influenced by dhurrin production in sorghum

Cyanogenic glucosides (CGs) play a key role in host-plant defense to insect feeding; however, the metabolic tradeoffs between synthesis of CGs and plant growth are not well understood. In this study, genetic mutants coupled with nondestructive phenotyping techniques were used to study the impact of the CG dhurrin on fall armyworm [Spodoptera frugiperda (J.E. Smith)] (FAW) feeding and plant growth in sorghum [Sorghum bicolor (L.) Moench]. A genetic mutation in CYP79A1 gene that disrupts dhurrin biosynthesis was used to develop sets of near-isogenic lines (NILs) with contrasting dhurrin contents in the Tx623 bmr6 genetic background. The NILs were evaluated for differences in plant growth and FAW feeding damage in replicated greenhouse and field trials. Greenhouse studies showed that dhurrin-free Tx623 bmr6 cyp79a1 plants grew more quickly than wild-type plants but were more susceptible to insect feeding based on changes in green plant area (GPA), total leaf area, and total dry weight over time. The NILs exhibited similar patterns of growth in field trials with significant differences in leaf area and dry weight of dhurrin-free plants between the infested and non-infested treatments. Taken together, these studies reveal a significant metabolic tradeoff between CG biosynthesis and plant growth in sorghum seedlings. Disruption of dhurrin biosynthesis produces plants with higher growth rates than wild-type plants but these plants have greater susceptibility to FAW feeding.

Seedling growth and fall armyworm feeding preference influenced by dhurrin production in sorghum

Cyanogenic glucosides (CGs) play a key role in host-plant defense to insect feeding; however, the metabolic tradeoffs between synthesis of CGs and plant growth are not well understood. In this study, genetic mutants coupled with nondestructive phenotyping techniques were used to study the impact of the CG dhurrin on fall armyworm [Spodoptera frugiperda (J.E. Smith)] (FAW) feeding and plant growth in sorghum [Sorghum bicolor (L.) Moench]. A genetic mutation in CYP79A1 gene that disrupts dhurrin biosynthesis was used to develop sets of near-isogenic lines (NILs) with contrasting dhurrin contents in the Tx623 bmr6 genetic background. The NILs were evaluated for differences in plant growth and FAW feeding damage in replicated greenhouse and field trials. Greenhouse studies showed that dhurrin-free Tx623 bmr6 cyp79a1 plants grew more quickly than wild-type plants but were more susceptible to insect feeding based on changes in green plant area (GPA), total leaf area, and total dry weight over time. The NILs exhibited similar patterns of growth in field trials with significant differences in leaf area and dry weight of dhurrin-free plants between the infested and non-infested treatments. Taken together, these studies reveal a significant metabolic tradeoff between CG biosynthesis and plant growth in sorghum seedlings. Disruption of dhurrin biosynthesis produces plants with higher growth rates than wild-type plants but these plants have greater susceptibility to FAW feeding.

Allelopathy as an evolutionary game

In plants, most competition is resource competition, where one plant simply preempts the resources away from its neighbors. Interference competition, as the name implies, is a form of direct interference to prevent resource access. Interference competition is common among animals that can physically fight, but in plants, one of the main mechanisms of interference competition is allelopathy. Allelopathic plants release cytotoxic chemicals into the environment which can increase their ability to compete with surrounding organisms for limited resources. The circumstances and conditions favoring the development and maintenance of allelochemicals, however, are not well understood. Particularly, despite the obvious benefits of allelopathy, current data suggest it seems to have only rarely evolved. To gain insight into the cost and benefit of allelopathy, we have developed a 2 × 2 matrix game to model the interaction between plants that produce allelochemicals and plants that do not. Production of an allelochemical introduces novel cost associated with both synthesis and detoxifying a toxic chemical but may also convey a competitive advantage. A plant that does not produce an allelochemical will suffer the cost of encountering one. Our model predicts three cases in which the evolutionarily stable strategies are different. In the first, the nonallelopathic plant is a stronger competitor, and not producing allelochemicals is the evolutionarily stable strategy. In the second, the allelopathic plant is the better competitor, and production of allelochemicals is the more beneficial strategy. In the last case, neither is the evolutionarily stable strategy. Instead, there are alternating stable states, depending on whether the allelopathic or nonallelopathic plant arrived first. The generated model reveals circumstances leading to the evolution of allelochemicals and sheds light on utilizing allelochemicals as part of weed management strategies. In particular, the wide region of alternative stable states in most parameterizations, combined with the fact that the absence of allelopathy is likely the ancestral state, provides an elegant answer to the question of why allelopathy seems to rarely evolve despite its obvious benefits. Allelopathic plants can indeed outcompete nonallelopathic plants, but this benefit is simply not great enough to allow them to go to fixation and spread through the population. Thus, most populations would remain purely nonallelopathic.

Integrative analysis of the shikonin metabolic network identifies new gene connections and reveals evolutionary insight into shikonin biosynthesis

Plant specialized 1,4-naphthoquinones present a remarkable case of convergent evolution. Species across multiple discrete orders of vascular plants produce diverse 1,4-naphthoquinones via one of several pathways using different metabolic precursors. Evolution of these pathways was preceded by events of metabolic innovation and many appear to share connections with biosynthesis of photosynthetic or respiratory quinones. Here, we sought to shed light on the metabolic connections linking shikonin biosynthesis with its precursor pathways and on the origins of shiknoin metabolic genes. Downregulation of Lithospermum erythrorhizon geranyl diphosphate synthase (LeGPPS), recently shown to have been recruited from a cytoplasmic farnesyl diphosphate synthase (FPPS), resulted in reduced shikonin production and a decrease in expression of mevalonic acid and phenylpropanoid pathway genes. Next, we used LeGPPS and other known shikonin pathway genes to build a coexpression network model for identifying new gene connections to shikonin metabolism. Integrative in silico analyses of network genes revealed candidates for biochemical steps in the shikonin pathway arising from Boraginales-specific gene family expansion. Multiple genes in the shikonin coexpression network were also discovered to have originated from duplication of ubiquinone pathway genes. Taken together, our study provides evidence for transcriptional crosstalk between shikonin biosynthesis and its precursor pathways, identifies several shikonin pathway gene candidates and their evolutionary histories, and establishes additional evolutionary links between shikonin and ubiquinone metabolism. Moreover, we demonstrate that global coexpression analysis using limited transcriptomic data obtained from targeted experiments is effective for identifying gene connections within a defined metabolic network.

Overexpression of arogenate dehydratase reveals an upstream point of metabolic control in phenylalanine biosynthesis

Out of the three aromatic amino acids, the highest flux in plants is directed towards phenylalanine, which is utilized to synthesize proteins and thousands of phenolic metabolites contributing to plant fitness. Phenylalanine is produced predominantly in plastids via the shikimate pathway and subsequent arogenate pathway, both of which are subject to complex transcriptional and post-transcriptional regulation. Previously, it was shown that allosteric feedback inhibition of arogenate dehydratase (ADT), which catalyzes the final step of the arogenate pathway, restricts flux through phenylalanine biosynthesis. Here, we show that in petunia (Petunia hybrida) flowers, which typically produce high phenylalanine levels, ADT regulation is relaxed, but not eliminated. Moderate expression of a feedback-insensitive ADT increased flux towards phenylalanine, while high overexpression paradoxically reduced phenylalanine formation. This reduction could be partially, but not fully, recovered by bypassing other known metabolic flux control points in the aromatic amino acid network. Using comparative transcriptomics, reverse genetics, and metabolic flux analysis, we discovered that transcriptional regulation of the d-ribulose-5-phosphate 3-epimerase gene in the pentose phosphate pathway controls flux into the shikimate pathway. Taken together, our findings reveal that regulation within and upstream of the shikimate pathway shares control over phenylalanine biosynthesis in the plant cell.

Convergent evolution of plant specialized 1,4-naphthoquinones: metabolism, trafficking, and resistance to their allelopathic effects

Plant 1,4-naphthoquinones encompass a class of specialized metabolites known to mediate numerous plant-biotic interactions. This class of compounds also presents a remarkable case of convergent evolution. The 1,4-naphthoquinones are synthesized by species belonging to nearly 20 disparate orders spread throughout vascular plants, and their production occurs via one of four known biochemically distinct pathways. Recent developments from large-scale biology and genetic studies corroborate the existence of multiple pathways to synthesize plant 1,4-naphthoquinones and indicate that extraordinary events of metabolic innovation and links to respiratory and photosynthetic quinone metabolism probably contributed to their independent evolution. Moreover, because many 1,4-naphthoquinones are excreted into the rhizosphere and they are highly reactive in biological systems, plants that synthesize these compounds also needed to independently evolve strategies to deploy them and to resist their effects. In this review, we highlight new progress made in understanding specialized 1,4-naphthoquinone biosynthesis and trafficking with a focus on how these discoveries have shed light on the convergent evolution and diversification of this class of compounds in plants. We also discuss how emerging themes in metabolism-based herbicide resistance may provide clues to mechanisms plants employ to tolerate allelopathic 1,4-naphthoquinones.

Evaluation of a Stable Isotope-Based Direct Quantification Method for Dicamba Analysis from Air and Water Using Single-Quadrupole LC-MS

Dicamba is a moderately volatile herbicide used for post-emergent control of broadleaf weeds in corn, soybean, and a number of other crops. With increased use of dicamba due to the release of dicamba-resistant cotton and soybean varieties, growing controversy over the effects of spray drift and volatilization on non-target crops has increased the need for quantifying dicamba collected from water and air sampling. Therefore, this study was designed to evaluate stable isotope-based direct quantification of dicamba from air and water samples using single-quadrupole liquid chromatography–mass spectrometry (LC–MS). The sample preparation protocols developed in this study utilize a simple solid-phase extraction (SPE) protocol for water samples and a single-step concentration protocol for air samples. The LC–MS detection method achieves sensitive detection of dicamba based on selected ion monitoring (SIM) of precursor and fragment ions and relies on the use of an isotopically labeled internal standard (IS) (D₃-dicamba), which allows for calculating recoveries and quantification using a relative response factor (RRF). Analyte recoveries of 106–128% from water and 88–124% from air were attained, with limits of detection (LODs) of 0.1 ng mL⁻¹ and 1 ng mL⁻¹, respectively. The LC–MS detection method does not require sample pretreatment such as ion-pairing or derivatization to achieve sensitivity. Moreover, this study reveals matrix effects associated with sorbent resin used in air sample collection and demonstrates how the use of an isotopically labeled IS with RRF-based analysis can account for ion suppression. The LC–MS method is easily transferrable and offers a robust alternative to methods relying on more expensive tandem LC–MS/MS-based options.

Hybrid de novo genome assembly of red gromwell (Lithospermum erythrorhizon) reveals evolutionary insight into shikonin biosynthesis

Lithospermum erythrorhizon (red gromwell; zicao) is a medicinal and economically valuable plant belonging to the Boraginaceae family. Roots from L. erythrorhizon have been used for centuries based on the antiviral and wound-healing properties produced from the bioactive compound shikonin and its derivatives. More recently, shikonin, its enantiomer alkannin, and several other shikonin/alkannin derivatives have collectively emerged as valuable natural colorants and as novel drug scaffolds. Despite several transcriptomes and proteomes having been generated from L. erythrorhizon, a reference genome is still unavailable. This has limited investigations into elucidating the shikonin/alkannin pathway and understanding its evolutionary and ecological significance. In this study, we obtained a de novo genome assembly for L. erythrorhizon using a combination of Oxford Nanopore long-read and Illumina short-read sequencing technologies. The resulting genome is ∼367.41 Mb long, with a contig N50 size of 314.31 kb and 27,720 predicted protein-coding genes. Using the L. erythrorhizon genome, we identified several additional p-hydroxybenzoate:geranyltransferase (PGT) homologs and provide insight into their evolutionary history. Phylogenetic analysis of prenyltransferases suggests that PGTs originated in a common ancestor of modern shikonin/alkannin-producing Boraginaceous species, likely from a retrotransposition-derived duplication event of an ancestral prenyltransferase gene. Furthermore, knocking down expression of LePGT1 in L. erythrorhizon hairy root lines revealed that LePGT1 is predominantly responsible for shikonin production early in culture establishment. Taken together, the reference genome reported in this study and the provided analysis on the evolutionary origin of shikonin/alkannin biosynthesis will guide elucidation of the remainder of the pathway.

SDG8-Mediated Histone Methylation and RNA Processing Function in the Response to Nitrate Signaling

Chromatin modification has gained increased attention for its role in the regulation of plant responses to environmental changes, but the specific mechanisms and molecular players remain elusive. Here, we show that the Arabidopsis (Arabidopsis thaliana) histone methyltransferase SET DOMAIN GROUP8 (SDG8) mediates genome-wide changes in H3K36 methylation at specific genomic loci functionally relevant to nitrate treatments. Moreover, we show that the specific H3K36 methyltransferase encoded by SDG8 is required for canonical RNA processing, and that RNA isoform switching is more prominent in the sdg8-5 deletion mutant than in the wild type. To demonstrate that SDG8-mediated regulation of RNA isoform expression is functionally relevant, we examined a putative regulatory gene, CONSTANS, CO-like, and TOC1 101 (CCT101), whose nitrogen-responsive isoform-specific RNA expression is mediated by SDG8. We show by functional expression in shoot cells that the different RNA isoforms of CCT101 encode distinct regulatory proteins with different effects on genome-wide transcription. We conclude that SDG8 is involved in plant responses to environmental nitrogen supply, affecting multiple gene regulatory processes including genome-wide histone modification, transcriptional regulation, and RNA processing, and thereby mediating developmental and metabolic processes related to nitrogen use.

Specialized naphthoquinones present in Impatiens glandulifera nectaries inhibit the growth of fungal nectar microbes

The invasion success of Impatiens glandulifera (Himalayan balsam) in certain parts of Europe and North America has been partially attributed to its ability to compete for bee pollinators with its rich nectar and due to its capacity to produce and release allelopathic 1,4-naphthoquinones (1,4-NQs) from its roots and leaves. Given that other 1,4-NQs present in the digestive fluids of certain carnivorous plants are proposed to control microbial colonization, we investigated the potential for the 1,4-NQs, 2-methoxy-1,4-naphthoquinone (2-MNQ) and lawsone, to fulfill an analogous role in the nectaries of I. glandulifera. Both 2-MNQ and lawsone were detected in the floral nectaries of I. glandulifera at levels comparable to leaves and roots, but were discovered to be at significantly higher levels in its extra-floral nectaries (EFNs) and to be present in EFN nectar itself. Nectar microbe inhibition assays revealed that the common nectar bacteria Gluconobacter oxydans and Asaia prunellae are not inhibited by 2-MNQ or lawsone, although both compounds were found to inhibit the growth of the common fungal nectar microbes Metschnikowia reukaufii and Aureobasidium pullulans. Taken together, these findings suggest that 2-MNQ and lawsone could serve to protect the rich nectar of I. glandulifera against fungal growth. The high abundance of 2-MNQ and lawsone in I. glandulifera EFNs may also point to an unsuspected mechanism for how allelopathic 1,4-NQs are leached into the soil where they exhibit their known allelopathic effects.

Contribution of isopentenyl phosphate to plant terpenoid metabolism

Plant genomes encode isopentenyl phosphate kinases (IPKs) that reactivate isopentenyl phosphate (IP) via ATP-dependent phosphorylation, forming the primary metabolite isopentenyl diphosphate (IPP) used generally for isoprenoid/terpenoid biosynthesis. Therefore, the existence of IPKs in plants raises unanswered questions concerning the origin and regulatory roles of IP in plant terpenoid metabolism. Here, we provide genetic and biochemical evidence showing that IP forms during specific dephosphorylation of IPP catalysed by a subset of Nudix superfamily hydrolases. Increasing metabolically available IP by overexpression of a bacterial phosphomevalonate decarboxylase (MPD) in Nicotiana tabacum resulted in significant enhancement in both monoterpene and sesquiterpene production. These results indicate that perturbing IP metabolism results in measurable changes in terpene products derived from both the methylerythritol phosphate (MEP) and mevalonate (MVA) pathways. Moreover, the unpredicted peroxisomal localization of bacterial MPD led us to discover that the step catalysed by phosphomevalonate kinase (PMK) imposes a hidden constraint on flux through the classical MVA pathway. These complementary findings fundamentally alter conventional views of metabolic regulation of terpenoid metabolism in plants and provide new metabolic engineering targets for the production of high-value terpenes in plants.

A peroxisomal thioesterase plays auxiliary roles in plant β-oxidative benzoic acid metabolism

Peroxisomal β-oxidative degradation of compounds is a common metabolic process in eukaryotes. Reported benzoyl-coenzyme A (BA-CoA) thioesterase activity in peroxisomes from petunia flowers suggests that, like mammals and fungi, plants contain auxiliary enzymes mediating β-oxidation. Here we report the identification of Petunia hybrida thioesterase 1 (PhTE1), which catalyzes the hydrolysis of aromatic acyl-CoAs to their corresponding acids in peroxisomes. PhTE1 expression is spatially, developmentally and temporally regulated and exhibits a similar pattern to known benzenoid metabolic genes. PhTE1 activity is inhibited by free coenzyme A (CoA), indicating that PhTE1 is regulated by the peroxisomal CoA pool. PhTE1 downregulation in petunia flowers led to accumulation of BA-CoA with increased production of benzylbenzoate and phenylethylbenzoate, two compounds which rely on the presence of BA-CoA precursor in the cytoplasm, suggesting that acyl-CoAs can be exported from peroxisomes. Furthermore, PhTE1 downregulation resulted in increased pools of cytoplasmic phenylpropanoid pathway intermediates, volatile phenylpropenes, lignin and anthocyanins. These results indicate that PhTE1 influences (i) intraperoxisomal acyl-CoA/CoA levels needed to carry out β-oxidation, (ii) efflux of β-oxidative products, acyl-CoAs and free acids, from peroxisomes, and (iii) flux distribution within the benzenoid/phenylpropanoid metabolic network. Thus, this demonstrates that plant thioesterases play multiple auxiliary roles in peroxisomal β-oxidative metabolism.

Emission of volatile organic compounds from petunia flowers is facilitated by an ABC transporter

Plants synthesize a diversity of volatile molecules that are important for reproduction and defense, serve as practical products for humans, and influence atmospheric chemistry and climate. Despite progress in deciphering plant volatile biosynthesis, their release from the cell has been poorly understood. The default assumption has been that volatiles passively diffuse out of cells. By characterization of a Petunia hybrida adenosine triphosphate-binding cassette (ABC) transporter, PhABCG1, we demonstrate that passage of volatiles across the plasma membrane relies on active transport. PhABCG1 down-regulation by RNA interference results in decreased emission of volatiles, which accumulate to toxic levels in the plasma membrane. This study provides direct proof of a biologically mediated mechanism of volatile emission.

The origin and biosynthesis of the naphthalenoid moiety of juglone in black walnut

Several members of the Juglandaceae family produce juglone, a specialized 1,4-naphthoquinone (1,4-NQ) natural product that is responsible for the notorious allelopathic effects of black walnut (Juglans nigra). Despite its documented ecological roles and potential for being developed as a novel natural product-based herbicide, none of the genes involved in synthesizing juglone have been identified. Based on classical labeling studies, we hypothesized that biosynthesis of juglone's naphthalenoid moiety is shared with biochemical steps of the phylloquinone pathway. Here, using comparative transcriptomics in combination with targeted metabolic profiling of 1,4-NQs in various black walnut organs, we provide evidence that phylloquinone pathway genes involved in 1,4-dihydroxynaphthoic acid (DHNA) formation are expressed in roots for synthesis of a compound other than phylloquinone. Feeding experiments using axenic black walnut root cultures revealed that stable isotopically labeled l-glutamate incorporates into juglone resulting in the same mass shift as that expected for labeling of the quinone ring in phylloquinone. Taken together, these results indicate that in planta, an intermediate from the phylloquinone pathway provides the naphthalenoid moiety of juglone. Moreover, this work shows that juglone can be de novo synthesized in roots without the contribution of immediate precursors translocated from aerial tissues. The present study illuminates all genes involved in synthesizing the juglone naphthoquinone ring and provides RNA-sequencing datasets that can be used with functional screening studies to elucidate the remaining juglone pathway genes. Translation of the generated knowledge is expected to inform future metabolic engineering strategies for harnessing juglone as a novel natural product-based herbicide.

Biosynthesis and molecular actions of specialized 1,4-naphthoquinone natural products produced by horticultural plants

The 1,4-naphthoquinones (1,4-NQs) are a diverse group of natural products found in every kingdom of life. Plants, including many horticultural species, collectively synthesize hundreds of specialized 1,4-NQs with ecological roles in plant-plant (allelopathy), plant-insect and plant-microbe interactions. Numerous horticultural plants producing 1,4-NQs have also served as sources of traditional medicines for hundreds of years. As a result, horticultural species have been at the forefront of many basic studies conducted to understand the metabolism and function of specialized plant 1,4-NQs. Several 1,4-NQ natural products derived from horticultural plants have also emerged as promising scaffolds for developing new drugs. In this review, the current understanding of the core metabolic pathways leading to plant 1,4-NQs is provided with additional emphasis on downstream natural products originating from horticultural species. An overview on the biochemical mechanisms of action, both from an ecological and pharmacological perspective, of 1,4-NQs derived from horticultural plants is also provided. In addition, future directions for improving basic knowledge about plant 1,4-NQ metabolism are discussed.

Rethinking how volatiles are released from plant cells

For plant volatile organic compounds (VOCs) to be emitted, they must cross membrane(s), the aqueous cell wall, and sometimes the cuticle, before moving into the gas phase. It is presumed that VOC movement through each barrier occurs via passive diffusion. However, VOCs, which are primarily nonpolar compounds, will preferentially partition into membranes, making diffusion into aqueous compartments slow. Using Fick's first law, we calculated that to achieve observed VOC emission rates by diffusion alone would necessitate toxic VOC levels in membranes. Here, we propose that biological mechanisms, such as those involved in trafficking other hydrophobic compounds, must contribute to VOC emission. Such parallel biological pathways would lower barrier resistances and, thus, steady-state emission rates could be maintained with significantly reduced intramembrane VOC concentrations.

A familiar ring to it: biosynthesis of plant benzoic acids

Plant benzoic acids (BAs) are building blocks or important structural elements for numerous primary and specialized metabolites, including plant hormones, cofactors, defense compounds, and attractants for pollinators and seed dispersers. Many natural products derived from plant BAs or containing benzoyl/benzyl moieties are also of medicinal or nutritional value to humans. Biosynthesis of BAs in plants is a network involving parallel and intersecting pathways spread across multiple subcellular compartments. In this review, a current overview on the metabolism of plant BAs is presented with a focus on the recent progress made on isolation and functional characterization of genes encoding biosynthetic enzymes and intracellular transporters. In addition, approaches for deciphering the complex interactions between pathways of the BAs network are discussed.

A Familiar Ring to It: Biosynthesis of Plant Benzoic Acids

Plant benzoic acids (BAs) are building blocks or important structural elements for numerous primary and specialized metabolites, including plant hormones, cofactors, defense compounds, and attractants for pollinators and seed dispersers. Many natural products derived from plant BAs or containing benzoyl/benzyl moieties are also of medicinal or nutritional value to humans. Biosynthesis of BAs in plants is a network involving parallel and intersecting pathways spread across multiple subcellular compartments. In this review, a current overview on the metabolism of plant BAs is presented with a focus on the recent progress made on isolation and functional characterization of genes encoding biosynthetic enzymes and intracellular transporters. In addition, approaches for deciphering the complex interactions between pathways of the BAs network are discussed.

An alternative pathway contributes to phenylalanine biosynthesis in plants via a cytosolic tyrosine:phenylpyruvate aminotransferase

Phenylalanine is a vital component of proteins in all living organisms, and in plants is a precursor for thousands of additional metabolites. Animals are incapable of synthesizing phenylalanine and must primarily obtain it directly or indirectly from plants. Although plants can synthesize phenylalanine in plastids through arogenate, the contribution of an alternative pathway via phenylpyruvate, as occurs in most microbes, has not been demonstrated. Here we show that plants also utilize a microbial-like phenylpyruvate pathway to produce phenylalanine, and flux through this route is increased when the entry point to the arogenate pathway is limiting. Unexpectedly, we find the plant phenylpyruvate pathway utilizes a cytosolic aminotransferase that links the coordinated catabolism of tyrosine to serve as the amino donor, thus interconnecting the extra-plastidial metabolism of these amino acids. This discovery uncovers another level of complexity in the plant aromatic amino acid regulatory network, unveiling new targets for metabolic engineering.

The Origin and Biosynthesis of the Benzenoid Moiety of Ubiquinone (Coenzyme Q) in Arabidopsis

It is not known how plants make the benzenoid ring of ubiquinone, a vital respiratory cofactor. Here, we demonstrate that Arabidopsis thaliana uses for that purpose two separate biosynthetic branches stemming from phenylalanine and tyrosine. Gene network modeling and characterization of T-DNA mutants indicated that acyl-activating enzyme encoded by At4g19010 contributes to the biosynthesis of ubiquinone specifically from phenylalanine. CoA ligase assays verified that At4g19010 prefers para-coumarate, ferulate, and caffeate as substrates. Feeding experiments demonstrated that the at4g19010 knockout cannot use para-coumarate for ubiquinone biosynthesis and that the supply of 4-hydroxybenzoate, the side-chain shortened version of para-coumarate, can bypass this blockage. Furthermore, a trans-cinnamate 4-hydroxylase mutant, which is impaired in the conversion of trans-cinnamate into para-coumarate, displayed similar defects in ubiquinone biosynthesis to that of the at4g19010 knockout. Green fluorescent protein fusion experiments demonstrated that At4g19010 occurs in peroxisomes, resulting in an elaborate biosynthetic architecture where phenylpropanoid intermediates have to be transported from the cytosol to peroxisomes and then to mitochondria where ubiquinone is assembled. Collectively, these results demonstrate that At4g19010 activates the propyl side chain of para-coumarate for its subsequent β-oxidative shortening. Evidence is shown that the peroxisomal ABCD transporter (PXA1) plays a critical role in this branch.

Functional convergence of structurally distinct thioesterases from cyanobacteria and plants involved in phylloquinone biosynthesis

The synthesis of phylloquinone (vitamin K1) in photosynthetic organisms requires a thioesterase that hydrolyzes 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA) to release 1,4-dihydroxy-2-naphthoate (DHNA). Cyanobacteria and plants contain distantly related hotdog-fold thioesterases that catalyze this reaction, although the structural basis of these convergent enzymatic activities is unknown. To investigate this, the crystal structures of hotdog-fold DHNA-CoA thioesterases from the cyanobacterium Synechocystis (Slr0204) and the flowering plant Arabidopsis thaliana (AtDHNAT1) were determined. These enzymes form distinct homotetramers and use different active sites to catalyze hydrolysis of DHNA-CoA, similar to the 4-hydroxybenzoyl-CoA (4-HBA-CoA) thioesterases from Pseudomonas and Arthrobacter. Like the 4-HBA-CoA thioesterases, the DHNA-CoA thioesterases contain either an active-site aspartate (Slr0204) or glutamate (AtDHNAT1) that are predicted to be catalytically important. Computational modeling of the substrate-bound forms of both enzymes indicates the residues that are likely to be involved in substrate binding and catalysis. Both enzymes are selective for DHNA-CoA as a substrate, but this selectivity is achieved using divergent predicted binding strategies. The Slr0204 binding pocket is predominantly hydrophobic and closely conforms to DHNA, while that of AtDHNAT1 is more polar and solvent-exposed. Considered in light of the related 4-HBA-CoA thioesterases, these structures indicate that hotdog-fold thioesterases using either an active-site aspartate or glutamate diverged into distinct clades prior to the evolution of strong substrate specificity in these enzymes.

Phylloquinone (vitamin K(1) ) biosynthesis in plants: two peroxisomal thioesterases of Lactobacillales origin hydrolyze 1,4-dihydroxy-2-naphthoyl-CoA

It is not known how plants cleave the thioester bond of 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA), a necessary step to form the naphthoquinone ring of phylloquinone (vitamin K(1) ). In fact, only recently has the hydrolysis of DHNA-CoA been demonstrated to be enzyme driven in vivo, and the cognate thioesterase characterized in the cyanobacterium Synechocystis. With a few exceptions in certain prokaryotic (Sorangium and Opitutus) and eukaryotic (Cyanidium, Cyanidioschyzon and Paulinella) organisms, orthologs of DHNA-CoA thioesterase are missing outside of the cyanobacterial lineage. In this study, genomic approaches and functional complementation experiments identified two Arabidopsis genes encoding functional DHNA-CoA thioesterases. The deduced plant proteins display low percentages of identity with cyanobacterial DHNA-CoA thioesterases, and do not even share the same catalytic motif. GFP-fusion experiments demonstrated that the Arabidopsis proteins are targeted to peroxisomes, and subcellular fractionations of Arabidopsis leaves confirmed that DHNA-CoA thioesterase activity occurs in this organelle. In vitro assays with various aromatic and aliphatic acyl-CoA thioester substrates showed that the recombinant Arabidopsis enzymes preferentially hydrolyze DHNA-CoA. Cognate T-DNA knock-down lines display reduced DHNA-CoA thioesterase activity and phylloquinone content, establishing in vivo evidence that the Arabidopsis enzymes are involved in phylloquinone biosynthesis. Extraordinarily, structure-based phylogenies coupled to comparative genomics demonstrate that plant DHNA-CoA thioesterases originate from a horizontal gene transfer with a bacterial species of the Lactobacillales order.

Contribution of CoA ligases to benzenoid biosynthesis in petunia flowers

Biosynthesis of benzoic acid from Phe requires shortening of the side chain by two carbons, which can occur via the β-oxidative or nonoxidative pathways. The first step in the β-oxidative pathway is cinnamoyl-CoA formation, likely catalyzed by a member of the 4-coumarate:CoA ligase (4CL) family that converts a range of trans-cinnamic acid derivatives into the corresponding CoA thioesters. Using a functional genomics approach, we identified two potential CoA-ligases from petunia (Petunia hybrida) petal-specific cDNA libraries. The cognate proteins share only 25% amino acid identity and are highly expressed in petunia corollas. Biochemical characterization of the recombinant proteins revealed that one of these proteins (Ph-4CL1) has broad substrate specificity and represents a bona fide 4CL, whereas the other is a cinnamate:CoA ligase (Ph-CNL). RNA interference suppression of Ph-4CL1 did not affect the petunia benzenoid scent profile, whereas downregulation of Ph-CNL resulted in a decrease in emission of benzylbenzoate, phenylethylbenzoate, and methylbenzoate. Green fluorescent protein localization studies revealed that the Ph-4CL1 protein is localized in the cytosol, whereas Ph-CNL is in peroxisomes. Our results indicate that subcellular compartmentalization of enzymes affects their involvement in the benzenoid network and provide evidence that cinnamoyl-CoA formation by Ph-CNL in the peroxisomes is the committed step in the β-oxidative pathway.

MutS HOMOLOG1 is a nucleoid protein that alters mitochondrial and plastid properties and plant response to high light

Mitochondrial-plastid interdependence within the plant cell is presumed to be essential, but measurable demonstration of this intimate interaction is difficult. At the level of cellular metabolism, several biosynthetic pathways involve both mitochondrial- and plastid-localized steps. However, at an environmental response level, it is not clear how the two organelles intersect in programmed cellular responses. Here, we provide evidence, using genetic perturbation of the MutS Homolog1 (MSH1) nuclear gene in five plant species, that MSH1 functions within the mitochondrion and plastid to influence organellar genome behavior and plant growth patterns. The mitochondrial form of the protein participates in DNA recombination surveillance, with disruption of the gene resulting in enhanced mitochondrial genome recombination at numerous repeated sequences. The plastid-localized form of the protein interacts with the plastid genome and influences genome stability and plastid development, with its disruption leading to variegation of the plant. These developmental changes include altered patterns of nuclear gene expression. Consistency of plastid and mitochondrial response across both monocot and dicot species indicate that the dual-functioning nature of MSH1 is well conserved. Variegated tissues show changes in redox status together with enhanced plant survival and reproduction under photooxidative light conditions, evidence that the plastid changes triggered in this study comprise an adaptive response to naturally occurring light stress.

A bimodular oxidoreductase mediates the specific reduction of phylloquinone (vitamin K₁) in chloroplasts

Plants and certain species of cyanobacteria are the only organisms capable of synthesizing phylloquinone (vitamin K₁ for vertebrates), which they use as an electron carrier during photosynthesis. Recent studies, however, have identified a plastidial pool of non-photoactive phylloquinone that could be involved in additional cellular functions. Here, we characterized an Arabidopsis bimodular enzyme--the At4g35760 gene product--comprising an integral domain homologous to the catalytic subunit of mammalian vitamin K₁ epoxide reductase (VKORC1, EC 1.1.4.1) that is fused to a soluble thioredoxin-like moiety. GFP-fusion experiments in tobacco mesophyll cells established that the plant protein is targeted to plastids, and analyses of transcript and protein levels showed that expression is maximal in leaf tissues. The fused and individual VKORC1 domains were separately expressed in yeast, removing their chloroplast targeting pre-sequence and adding a C-terminal consensus signal for retention in the endoplasmic reticulum. The corresponding microsomal preparations were equally effective at mediating the dithiotreitol-dependent reduction of phylloquinone and menaquinone into their respective quinol forms. Strikingly, unlike mammalian VKORC1, the Arabidopsis enzyme did not reduce phylloquinone epoxide, and was resistant to inhibition by warfarin. The isoprenoid benzoquinone conjugates plastoquinone and ubiquinone were not substrates, establishing that the plant enzyme evolved strict specificity for the quinone form of naphthalenoid conjugates. In vitro reconstitution experiments established that the soluble thioredoxin-like domain can function as an electron donor for its integral VKORC1 partner.

Detection and quantification of vitamin K(1) quinol in leaf tissues

Phylloquinone (2-methyl-3-phytyl-1,4-naphthoquinone; vitamin K(1)) is vital to plants. It is responsible for the one-electron transfer at the A(1) site of photosystem I, a process that involves turnover between the quinone and semi-quinone forms of phylloquinone. Using HPLC coupled with fluorometric detection to analyze Arabidopsis leaf extracts, we detected a third redox form of phylloquinone corresponding to its fully reduced - quinol-naphthoquinone ring (PhQH(2)). A method was developed to quantify PhQH(2) and its corresponding oxidized quinone (PhQ) counterpart in a single HPLC run. PhQH(2) was found in leaves of all dicotyledonous and monocotyledonous species tested, but not in fruits or in tubers. Its level correlated with that of PhQ, and represented 5-10% of total leaf phylloquinone. Analysis of purified pea chloroplasts showed that these organelles accounted for the bulk of PhQH(2). The respective pool sizes of PhQH(2) and PhQ were remarkably stable throughout the development of Arabidopsis green leaves. On the other hand, in Arabidopsis and tomato senescing leaves, PhQH(2) was found to increase at the expense of PhQ, and represented 25-35% of the total pool of phylloquinone. Arabidopsis leaves exposed to light contained lower level of PhQH(2) than those kept in the dark. These data indicate that PhQH(2) does not originate from the photochemical reduction of PhQ, and point to a hitherto unsuspected function of phylloquinone in plants. The putative origin of PhQH(2) and its recycling into PhQ are discussed.