Steroidal scaffold decorations in Solanum alkaloid biosynthesis

Molecular characterization and structural basis of a promiscuous glycosyltransferase for β-(1,6) oligoglucoside chain glycosides biosynthesis

Sugar building blocks are crucial for the chemical diversity and biological activity of secondary metabolites. UDP-dependent glycosyltransferases (UGTs) play a pivotal role in the biosynthesis of glycosides in plants by catalysing the attachment of sugar moieties to various bioactive natural products. However, the biosynthesis of oligosaccharide-chain glycosides is often limited by the narrow substrate specificity of UGTs. In this study, we identify a regio-specific β-(1,6) glycosyltransferase, UGT94BY1, from Platycodon grandiflorum. UGT94BY1 exhibits broad substrate promiscuity and can transfer up to three sugar moieties to the C6-OH position of the glucosyl group in various triterpenoids and phenolic glycosides, thereby forming β-(1,6) oligoglucoside chains. To elucidate the mechanism underlying its substrate selectivity, we determined the crystal structure of the UGT94BY1 complex with UDP at a resolution of 2.0 Å. Molecular simulations revealed that a critical structural motif, comprising residues N84-M91, S141-L155 and R179-E186, plays a key role in recognizing sugar acceptors and facilitating chain elongation. Our study unveils a powerful glycosyltransferase for β-(1,6) oligoglucoside chain biosynthesis and highlights key regions involved in substrate recognition and sugar chain extension, providing valuable insights for designing UGTs with customized substrate specificities for biotechnological applications.

Genome-wide association study identifies candidate genes for glycoalkaloid biosynthesis in tetraploid potato (Solanum tuberosum L.) tubers

BACKGROUND

Steroidal glycoalkaloids (SGAs), derived from cholesterol, act as natural defenses against pathogens and pests. In cultivated potatoes, α-solanine and α-chaconine are the primary SGAs, distributed throughout the plant, with their biosynthesis mechanisms differing across various tissues. The variation in SGAs content between the cortex and perimedullary zone reflects tissue-specific metabolic regulation in potato tuber. Higher SGAs levels in the cortex may enhance defense against external threats. This spatial distribution provides a theoretical basis for breeding strategies aimed at balancing resistance and food quality by regulating SGAs accumulation in specific tissues of potato tubers. Excessive levels of SGAs in potato tubers can compromise both their quality and edibility. Additionally, SGAs exhibit pharmacological properties, including anti-protozoal, antibacterial, antiviral, anti-tumor, and anti-inflammatory effects.

RESULTS

This study conducted genome-wide association study (GWAS) on SGAs content in the cortex and perimedullary zone of 117 diverse potato germplasm accessions, utilizing 22,983,689 high-quality SNPs. Candidate genes were subjected to analyses of stability, pleiotropy, GO and KEGG enrichment, and haplotype profiling. Twelve candidate genes associated with SGAs biosynthesis in potato tubers were identified, encoding UDP-glycosyltransferase superfamily proteins (Soltu.DM.11G005750, Soltu.DM.11G005760, Soltu.DM.11G005770, Soltu.DM.11G005820), fatty acid hydroxylase superfamily proteins (Soltu.DM.01G029600, Soltu.DM.01G029610, Soltu.DM.01G029620, Soltu.DM.01G029640, Soltu.DM.01G029650, Soltu.DM.10G008360), alkaline/neutral invertase (Soltu.DM.11G006090), and pleiotropic drug resistance (Soltu.DM.11G006080).

CONCLUSIONS

This study provides a theoretical basis for elucidating the genetic mechanisms underlying SGAs biosynthesis in potatoes and will facilitate the breeding of new potato varieties.

An Effective Computational Strategy for UGTs Catalytic Function Prediction

The GT-B type glycosyltransferases play a crucial post-modification role in synthesizing natural products, such as triterpenoid and steroidal saponins, renowned for their diverse pharmacological activities. Despite phylogenetic analysis aiding in enzyme family classification, distinguishing substrate specificity between triterpenoid and steroidal saponins, with their highly similar cyclic scaffolds, remains a formidable challenge. Our studies unveil the potential transport tunnels for the glycosyl donor and acceptor in PpUGT73CR1, by molecular dynamics simulations. This revelation leads to a plausible substrate transport mechanism, highlighting the regulatory role of the N-terminal domain (NTD) in glycosyl acceptor binding and transport. Inspired by these structural and mechanistic insights, we further analyze the binding pockets of 44 plant-derived UGTs known to glycosylate triterpenes and sterols. Notably, sterol UGTs are found to harbor aromatic and hydrophobic residues with polar residues typically present at the bottom of the active pocket. Drawing inspiration from the substrate binding and product release mechanism revealed through structure-based molecular modeling, we devised a fast sequence-based method for classifying UGTs using the pre-trained ESM2 protein model. This method involved extracting the NTD features of UGTs and performing PCA clustering analysis, enabling accurate identification of enzyme function, and even differentiation of substrate specificity/promiscuity between structurally similar triterpenoid and steroidal substrates, which is further validated by experiments. This work not only deepens our understanding of substrate binding mechanisms but also provides an effective computational protocol for predicting the catalytic function of unknown UGTs.

Alkaloid evolution in the Solanaceae

Alkaloids are a diverse class of nitrogen-containing metabolites involved in key biotic interactions, such as defense against herbivores and pathogens and the recruitment of pollinators. The Solanaceae family has served as a model for studying alkaloid evolution, due to the varied types of alkaloids it produces, such as nicotinoids, tropane alkaloids (TAs), steroidal glycoalkaloids (SGAs), and capsaicinoids. Recent multi-omics and comparative genomics studies have expanded our understanding of the genetic and evolutionary mechanisms driving alkaloid diversification. These metabolites are produced by specific clades within the family, often in response to selective pressures such as herbivore and pathogen coevolution, which shape alkaloid profiles through both diversification and reduction. Evolutionary processes like genome duplications, rearrangements, and introgressions have also played a significant role in the emergence of new alkaloid pathways, promoting metabolic adaptations. The Solanaceae family exhibits both convergence and divergence in alkaloid production, with certain alkaloids arising independently in different lineages. Notably, biosynthetic gene clusters (BGCs) and gene duplication have been linked to alkaloid diversification, with the structure and function of these regions driving metabolic variability. Furthermore, human domestication of plants such as tobacco and chili peppers has influenced the alkaloid profiles of crop species, particularly in terms of pest resistance and flavor. The evolution of alkaloids in this family has not only shaped plant defense mechanisms but also has important implications for human health and agriculture. This review highlights the dynamic interplay between genetics, ecology, and human influence in the evolution of alkaloids within the Solanaceae family.

A noncanonical scaffold in steroidal metabolism

A recent study by Boccia et al. identified GAME15, a cellulose synthase-like protein that is essential for steroidal saponin and glycoalkaloid biosynthesis in Solanum species. GAME15 functions as a scaffold, interacting with key enzymes involved in the early steps of biosynthesis, enabling metabolic flux from cholesterol to steroidal defense compounds.

Navigating the challenges of engineering composite specialized metabolite pathways in plants

Plants are a valuable source of diverse specialized metabolites with numerous applications. However, these compounds are often produced in limited quantities, particularly under unfavorable ecological conditions. To achieve sufficient levels of target metabolites, alternative strategies such as pathway engineering in heterologous systems like microbes (e.g., bacteria and fungi) or cell-free systems can be employed. Another approach is plant engineering, which aims to either enhance the native production in the original plant or reconstruct the target pathway in a model plant system. Although increasing metabolite production in the native plant is a promising strategy, these source plants are often exotic and pose significant challenges for genetic manipulation. Effective pathway engineering requires comprehensive prior knowledge of the genes and enzymes involved, as well as the precursor, intermediate, branching, and final metabolites. Thus, a thorough elucidation of the biosynthetic pathway is closely linked to successful metabolic engineering in host or model systems. In this review, we highlight recent advances in strategies for biosynthetic pathway elucidation and metabolic engineering. We focus on efforts to engineer complex, multi-step pathways that require the expression of at least eight genes for transient and three genes for stable transformation. Reports on the engineering of complex pathways in stably transformed plants remain relatively scarce. We discuss the major hurdles in pathway elucidation and strategies for overcoming them, followed by an overview of achievements, challenges, and solutions in pathway reconstitution through metabolic engineering. Recent advances including computer-based predictions offer valuable platforms for the sustainable production of specialized metabolites in plants.

A scaffold protein manages the biosynthesis of steroidal defense metabolites in plants

Solanaceae plants produce two major classes of valuable sterol-derived natural products-steroidal glycoalkaloids and steroidal saponins-from a common cholesterol precursor. Attempts to heterologously produce these molecules have consistently failed, although the genes responsible for each biosynthetic step have been identified. Here we identify a cellulose synthase-like protein, an unexpected biosynthetic component that interacts with the early pathway enzymes, enabling steroidal scaffolds production in plants. Moreover, knockout of this gene in black nightshade, Solanum nigrum, resulted in plants lacking both steroidal alkaloids and saponins. Unexpectedly, these knockout plants also revealed that steroidal saponins deter serious agricultural insect pests. This discovery provides the missing link to engineer these high-value steroidal molecules and also pinpoints the ecological role for steroidal saponins.

Potato steroidal glycoalkaloids: properties, biosynthesis, regulation and genetic manipulation

Steroidal glycoalkaloids (SGAs), predominantly comprising α-solanine (C45H73NO15) and α-chaconine (C45H73NO14), function as natural phytotoxins within potatoes. In addition to their other roles, these SGAs are crucial for enabling potato plants to withstand biotic stresses. However, they also exhibit toxicity towards humans and animals. Consequently, the content and distribution of SGAs are crucial traits for the genetic improvement of potatoes. This review focuses on advancing research related to the biochemical properties, biosynthesis, regulatory mechanisms, and genetic improvement of potato SGAs. Furthermore, we provide perspectives on future research directions to further enhance our understanding of SGA biosynthesis and regulation, ultimately facilitating the targeted development of superior potato varieties.