Exploiting enzyme promiscuity to shape plant specialized metabolism

Overexpression and RNAi-mediated Knockdown of Two 3β-hydroxy-Δ5-steroid dehydrogenase Genes in Digitalis lanata Shoot Cultures Reveal Their Role in Cardenolide Biosynthesis

3β-hydroxy-Δ5-steroid dehydrogenases (3βHSDs) are supposed to be involved in 5β-cardenolide biosynthesis. Here, a novel 3βHSD (Dl3βHSD2) was isolated from Digitalis lanata shoot cultures and expressed in E. coli. Recombinant Dl3βHSD1 and Dl3βHSD2 shared 70% amino acid identity, reduced various 3-oxopregnanes and oxidised 3-hydroxypregnanes, but only rDl3βHSD2 converted small ketones and secondary alcohols efficiently. To explain these differences in substrate specificity, we established homology models using borneol dehydrogenase of Salvia rosmarinus (6zyz) as the template. Hydrophobicity and amino acid residues in the binding pocket may explain the difference in enzyme activities and substrate preferences. Compared to Dl3βHSD1, Dl3βHSD2 is weakly expressed in D. lanata shoots. High constitutive expression of Dl3βHSDs was realised by Agrobacterium-mediated transfer of Dl3βHSD genes fused to the CaMV-35S promotor into the genome of D. lanata wild type shoot cultures. Transformed shoots (35S:Dl3βHSD1 and 35S:Dl3βHSD2) accumulated less cardenolides than controls. The levels of reduced glutathione (GSH), which is known to inhibit cardenolide formation, were higher in the 35S:Dl3βHSD1 lines than in the controls. In the 35S:Dl3βHSD1 lines cardenolide levels were restored after adding of the substrate pregnane-3,20-dione in combination with buthionine-sulfoximine (BSO), an inhibitor of GSH formation. RNAi-mediated knockdown of the Dl3βHSD1 yielded several shoot culture lines with strongly reduced cardenolide levels. In these lines, cardenolide biosynthesis was fully restored after addition of the downstream precursor pregnan-3β-ol-20-one, whereas upstream precursors such as progesterone had no effect, indicating that no shunt pathway could overcome the Dl3βHSD1 knockdown. These results can be taken as the first direct proof that Dl3βHSD1 is indeed involved in 5β-cardenolide biosynthesis.

Diversity and divergence: evolution of secondary metabolism in the tropical tree genus Inga

Plants are widely recognized as chemical factories, with each species producing dozens to hundreds of unique secondary metabolites. These compounds shape the interactions between plants and their natural enemies. We explore the evolutionary patterns and processes by which plants generate chemical diversity, from evolving novel compounds to unique chemical profiles. We characterized the chemical profile of one-third of the species of tropical rainforest trees in the genus Inga (c. 100, Fabaceae) using ultraperformance liquid chromatography-mass spectrometry-based metabolomics and applied phylogenetic comparative methods to understand the mode of chemical evolution. We show: each Inga species contain structurally unrelated compounds and high levels of phytochemical diversity; closely related species have divergent chemical profiles, with individual compounds, compound classes, and chemical profiles showing little-to-no phylogenetic signal; at the evolutionary time scale, a species' chemical profile shows a signature of divergent adaptation. At the ecological time scale, sympatric species were the most divergent, implying it is also advantageous to maintain a unique chemical profile from community members; finally, we integrate these patterns with a model for how chemical diversity evolves. Taken together, these results show that phytochemical diversity and divergence are fundamental to the ecology and evolution of plants.

Using interdisciplinary, phylogeny-guided approaches to understand the evolution of plant metabolism

To cope with relentless environmental pressures, plants produce an arsenal of structurally diverse chemicals, often called specialized metabolites. These lineage-specific compounds are derived from the simple building blocks made by ubiquitous core metabolic pathways. Although the structures of many specialized metabolites are known, the underlying metabolic pathways and the evolutionary events that have shaped the plant chemical diversity landscape are only beginning to be understood. However, with the advent of multi-omics data sets and the relative ease of studying pathways in previously intractable non-model species, plant specialized metabolic pathways are now being systematically identified. These large datasets also provide a foundation for comparative, phylogeny-guided studies of plant metabolism. Comparisons of metabolic traits and features like chemical abundances, enzyme activities, or gene sequences from phylogenetically diverse plants provide insights into how metabolic pathways evolved. This review highlights the power of studying evolution through the lens of comparative biochemistry, particularly how placing metabolism into a phylogenetic context can help a researcher identify the metabolic innovations enabling the evolution of structurally diverse plant metabolites.

Substrate promiscuity of acyltransferases contributes to the diversity of hydroxycinnamic acid derivatives in purple coneflower

High pliability and promiscuity are observed widely exist in plant specialized metabolism, especially the hydroxycinnamic acid metabolism. Here, we identified an addition BAHD acyltransferase (EpHMT) that catalyzes phaselic acid biosynthesis and found that the substrate promiscuities of identified BAHD and SCPL acyltransferases are responsible for the diversity of hydroxycinnamic acid derivatives in purple coneflower.

2-oxoglutarate-dependent dioxygenases drive expansion of steroidal alkaloid structural diversity in the genus Solanum

Solanum steroidal glycoalkaloids (SGAs) are renowned defence metabolites exhibiting spectacular structural diversity. Genes and enzymes generating the SGA precursor pathway, SGA scaffold and glycosylated forms have been largely identified. Yet, the majority of downstream metabolic steps creating the vast repertoire of SGAs remain untapped. Here, we discovered that members of the 2-OXOGLUTARATE-DEPENDENT DIOXYGENASE (2-ODD) family play a prominent role in SGA metabolism, carrying out three distinct backbone-modifying oxidative steps in addition to the three formerly reported pathway reactions. The GLYCOALKALOID METABOLISM34 (GAME34) enzyme catalyses the conversion of core SGAs to habrochaitosides in wild tomato S. habrochaites. Cultivated tomato plants overexpressing GAME34 ectopically accumulate habrochaitosides. These habrochaitoside enriched plants extracts potently inhibit Puccinia spp. spore germination, a significant Solanaceae crops fungal pathogen. Another 2-ODD enzyme, GAME33, acts as a desaturase (via hydroxylation and E/F ring rearrangement) forming unique, yet unreported SGAs. Conversion of bitter α-tomatine to ripe fruit, nonbitter SGAs (e.g. esculeoside A) requires two hydroxylations; while the known GAME31 2-ODD enzyme catalyses hydroxytomatine formation, we find that GAME40 catalyses the penultimate step in the pathway and generates acetoxy-hydroxytomatine towards esculeosides accumulation. Our results highlight the significant contribution of 2-ODD enzymes to the remarkable structural diversity found in plant steroidal specialized metabolism.

Chiral carbon dots - a functional domain for tyrosinase Cu active site modulation via remote target interaction

The nano-hybrid enzyme is an ideal catalytic system that integrates various advantages from biocatalysis and nanocatalysis into homogeneous and heterogeneous catalysis. However, great efforts are still needed to fully understand the interactions between nanoparticles and enzymes. Here, we show chiral carbon dots (CDs) as a new functional domain for tyrosinase Cu active site modulation via remote target interaction. Three kinds of chiral CDs (LCDs-1/-2/-3; DCDs-1/-2/-3) were fabricated by thermal treatment of citric acid and L/D-aspartic acid. Then a series of CDs/tyrosinase composites (namely, nano-hybrid-enzymes) were prepared, demonstrating good regulation of enzyme catalytic kinetics. Especially, we find that LCDs-1 is an irreversible inhibitor with great inhibition effect while the others are all reversible inhibitors. Furthermore, it is suggested by both experiments and all-atom molecular dynamics simulations that the joint effect of LCDs-1 and tyrosinase makes LCDs-1 serve as a new functional domain, which has a distinguished ability to control the conformational changes of the key sites of the active center of the tyrosinase (e.g., H60) and thus the escaping behavior of copper ions and the catalytic activity. This work opens a new route for nano-hybrid-enzyme design and enzyme activity regulation with chiral carbon materials as functional domains via remote target interaction.

Knockout of Arabidopsis thaliana VEP1, Encoding a PRISE (Progesterone 5β-Reductase/Iridoid Synthase-Like Enzyme), Leads to Metabolic Changes in Response to Exogenous Methyl Vinyl Ketone (MVK)

Small or specialized natural products (SNAPs) produced by plants vary greatly in structure and function, leading to selective advantages during evolution. With a limited number of genes available, a high promiscuity of the enzymes involved allows the generation of a broad range of SNAPs in complex metabolic networks. Comparative metabolic studies may help to understand why—or why not—certain SNAPs are produced in plants. Here, we used the wound-induced, vein patterning regulating VEP1 (AtStR1, At4g24220) and its paralogue gene on locus At5g58750 (AtStR2) from Arabidopsis to study this issue. The enzymes encoded by VEP1-like genes were clustered under the term PRISEs (progesterone 5β-reductase/iridoid synthase-like enzymes) as it was previously demonstrated that they are involved in cardenolide and/or iridoid biosynthesis in other plants. In order to further understand the general role of PRISEs and to detect additional more “accidental” roles we herein characterized A. thaliana steroid reductase 1 (AtStR1) and compared it to A. thaliana steroid reductase 2 (AtStR2). We used A. thaliana Col-0 wildtype plants as well as VEP1 knockout mutants and VEP1 knockout mutants overexpressing either AtStR1 or AtStR2 to investigate the effects on vein patterning and on the stress response after treatment with methyl vinyl ketone (MVK). Our results added evidence to the assumption that AtStR1 and AtStR2, as well as PRISEs in general, play specific roles in stress and defense situations and may be responsible for sudden metabolic shifts.

Origin and Function of Structural Diversity in the Plant Specialized Metabolome

The plant specialized metabolome consists of a multitude of structurally and functionally diverse metabolites, variable from species to species. The specialized metabolites play roles in the response to environmental changes and abiotic or biotic stresses, as well as in plant growth and development. At its basis, the specialized metabolism is built of four major pathways, each starting from a few distinct primary metabolism precursors, and leading to distinct basic carbon skeleton core structures: polyketides and fatty acid derivatives, terpenoids, alkaloids, and phenolics. Structural diversity in specialized metabolism, however, expands exponentially with each subsequent modification. We review here the major sources of structural variety and question if a specific role can be attributed to each distinct structure. We focus on the influences that various core structures and modifications have on flavonoid antioxidant activity and on the diversity generated by oxidative coupling reactions. We suggest that many oxidative coupling products, triggered by initial radical scavenging, may not have a function in se, but could potentially be enzymatically recycled to effective antioxidants. We further discuss the wide structural variety created by multiple decorations (glycosylations, acylations, prenylations), the formation of high-molecular weight conjugates and polyesters, and the plasticity of the specialized metabolism. We draw attention to the need for untargeted methods to identify the complex, multiply decorated and conjugated compounds, in order to study the functioning of the plant specialized metabolome.

21-Hydroxypregnane 21-O-malonylation, a crucial step in cardenolide biosynthesis, can be achieved by substrate-promiscuous BAHD-type phenolic glucoside malonyltransferases from Arabidopsis thaliana and homolog proteins from Digitalis lanata

Three putative 21-hydroxypregnane 21-O-malonyltransferases (21MaT) from Digitalis lanata were partially purified. Two of them were supposed to be BAHD-type enzymes. We were unable to purify them in quantities necessary for reliable sequencing. We identified two genes in A. thaliana coding for substrate-promiscuous BAHD-type phenolic glucoside malonyltransferases (AtPMaT1, AtPMaT2) and docked various 21-hydroxypregnanes into the substrate-binding site of a homology model built on the BAHD template 2XR7 (NtMaT1 from N. tabacum). Recombinant forms of Atpmat1 and Atpmat2 were expressed in E. coli and the recombinant enzymes characterized with regard to their substrate preferences. They were shown to malonylate various 21-hydroxypregnanes. The Atpmat1 sequence was used to identify candidate genes in Digitalis lanata (Dlmat1 to Dlmat4). Dlmat1 and Dlmat2 were also expressed in E. coli and shown to possess 21-hydroxypregnane 21-O-malonyltransferase activity.

Silent constraints: the hidden challenges faced in plant metabolic engineering

Metabolic engineering is embraced as a method to sustainably enhance production of valuable phytochemicals with beneficial properties. However, successful production of these compounds in plants is not always predictable even when the pathways are fully known, frequently due to the lack of comprehensive understanding of plant metabolism as a whole, and interconnections between different primary, secondary, and hormone metabolic networks. Here, we highlight critical hidden constraints, including substrate availability, silent metabolism, and metabolic crosstalk, that impair engineering strategies. We explore how these constraints have historically been manifested in engineering attempts and propose how modern advancements will enable future strategies to overcome these impediments.

Managing enzyme promiscuity in plant specialized metabolism: A lesson from flavonoid biosynthesis: Mission of a "body double" protein clarified

Specificities of enzymes involved in plant specialized metabolism, including flavonoid biosynthesis, are generally promiscuous. This enzyme promiscuity has served as an evolutionary basis for new enzyme functions and metabolic pathways in land plants adapting to environmental challenges. This phenomenon may lead, however, to inefficiency in specialized metabolism and adversely affect metabolite-mediated plant survival. How plants manage enzyme promiscuity for efficient specialized metabolism is, thus, an open question. Recent studies of flavonoid biosynthesis addressing this issue have revealed a conserved strategy, namely, a homolog of chalcone isomerase with no catalytic activity binds to chalcone synthase, a key flavonoid pathway enzyme, to narrow (or rectify) the enzyme's highly promiscuous product specificity. Reducing promiscuity via specific protein-protein interactions among metabolic enzymes and proteins may be a solution adopted by land plants to achieve efficient operation of specialized metabolism, while the intrinsic promiscuity of enzymes has likely been retained incidentally.

Evolutionary dynamics of natural product biosynthesis in bacteria

Covering: 2008 up to 2019The forces of biochemical adaptive evolution operate at the level of genes, manifesting in complex phenotypes and the global biodiversity of proteins and metabolites. While evolutionary histories have been deciphered for some other complex traits, the origins of natural product biosynthesis largely remain a mystery. This fundamental knowledge gap is surprising given the many decades of research probing the genetic, chemical, and biophysical mechanisms of bacterial natural product biosynthesis. Recently, evolutionary thinking has begun to permeate this otherwise mechanistically dominated field. Natural products are now sometimes referred to as 'specialized' rather than 'secondary' metabolites, reinforcing the importance of their biological and ecological functions. Here, we review known evolutionary mechanisms underlying the overwhelming chemical diversity of bacterial secondary metabolism, focusing on enzyme promiscuity and the evolution of enzymatic domains that enable metabolic traits. We discuss the mechanisms that drive the assembly of natural product biosynthetic gene clusters and propose formal definitions for 'specialized' and 'secondary' metabolism. We further explore how biosynthetic gene clusters evolve to synthesize related molecular species, and in turn how the biological and ecological roles that emerge from metabolic diversity are acted on by selection. Finally, we reconcile chemical, functional, and genetic data into an evolutionary model, the dynamic chemical matrix evolutionary hypothesis, in which the relationships between chemical distance, biomolecular activity, and relative fitness shape adaptive landscapes.

Directed Evolution of Plant Processes: Towards a Green (r)Evolution?

Directed evolution (DE) is a powerful approach for generating proteins with new chemical and physical properties. It mimics the principles of Darwinian evolution by imposing selective pressure on a large population of molecules harboring random genetic variation in DNA, such that sequences with specific desirable properties are generated and selected. We propose that combining DE and genome-editing (DE-GE) technologies represents a powerful tool to discover and integrate new traits into plants for agronomic and biotechnological gain. DE-GE has the potential to deliver a new green (r)evolution research platform that can provide novel solutions to major trait delivery aspirations for sustainable agriculture, climate-resilient crops, and improved food security and nutritional quality.

Horizontal Natural Product Transfer: Intriguing Insights into a Newly Discovered Phenomenon

Just recently, the "horizontal natural product transfer" was unveiled: alkaloids, which have been leached out from decomposing alkaloidal donor plants, are taken up by the roots of acceptor plants. In the same manner, many other natural products, such as coumarins or stilbenes, are also taken up from the soil. Recent research outlined that alkaloids are transferred also from a living donor plant to plants growing in their vicinity. In the acceptor plants, the imported natural products might be modified by hydroxylation and glucosylation. These insights will strongly impact our understanding of contamination of plant-derived commodities as well as plant-plant interactions.