Two diversities meet in the rhizosphere:root specialized metabolites and microbiome

Plants serve as rich repositories of diverse chemical compounds collectively referred to as specialized metabolites.These compounds are of importance for adaptive processes,including interactions with various microbes both beneficial and harmful.Considering microbes as bioreactors,the chemical diversity undergoes dynamic changes when root-derived specialized metabolites(RSMs)and microbes encounter each other in the rhizosphere.Recent advancements in sequencing techniques and molecular biology tools have not only accelerated the elucidation of biosynthetic pathways of RSMs but also unveiled the significance of RSMs in plant-microbe interactions.In this review,we provide a comprehensive description of the effects of RSMs on microbe assembly in the rhizosphere and the influence of corresponding microbial changes on plant health,incorporating the most up-to-date information available.Additionally,we highlight open questions that remain for a deeper understanding of and harnessing the potential of RSM-microbe interactions to enhance plant adaptation to the environment.Finally,we propose a pipeline for investigating the intricate associations between root exometabolites and the rhizomicrobiome.

Functional diversity and metabolic engineering of plantspecialized metabolites

Plants are talented biochemists that produce a broad diversity of small molecules.These so-called specialized metabolites(SMs)play critical roles in the adaptive evolution of plants to defend against biotic and abiotic stresses,attract pollinators,and modulate soil microbiota for their own benefits.Many plant SMs have been used as nutrition and flavor compounds in our daily food,as well as drugs for treatment of human diseases.Current multi-omics tools have significantly accelerated the process of biosynthetic pathway elucidation in plants through correlation analyses,genetic mapping,and de novo biosynthetic gene cluster predictions.Understanding the biosynthesis of plant SMs has enabled reconstitution of naturally occurring specialized metabolic pathways in microbial hosts,providing a sustainable supply of these high-value molecules.In this review,we illustrate the general functions of several typical plant SMs in natural ecosystems and for human societies.We then provide an overview of current methods elucidating the biosynthetic pathways of plant SMs,and synthetic biology strategies that optimize the efficiency of heterologous biosynthetic pathways in microbial hosts.Moving forward,dissection of the functions and application of plant SMs by using current multidiscipline approaches would be greatly benefit to the scientific community and human societies.

Steroidal scaffold decorations in Solanum alkaloid biosynthesis

Steroidal glycoalkaloids(SGAs)are specialized metabolites produced by hundreds of Solanum species,including important vegetable crops such as tomato,potato,and eggplant.Although it has been known that SGAs play important roles in defense in plants and“anti-nutritional"effects(e.g.,toxicity and bitterness)to humans,many of these molecules have documented anti-cancer,anti-microbial,antiinflammatory,anti-viral,and anti-pyretic activities.Among these,α-solasonine andα-solamargine isolated from black nightshade(Solanum nigrum)are reported to have potent anti-tumor,anti-proliferative,and anti-inflammatory activities.Notably,α-solasonine andα-solamargine,along with the core steroidal aglycone solasodine,are the most widespread SGAs produced among the Solanum plants.However,it is still unknown how plants synthesize these bioactive steroidal molecules.Through comparative metabolomictranscriptome-guided approach,biosynthetic logic,combinatorial expression in Nicotiana benthamiana,and functional recombinant enzyme assays,here we report the discovery of 12 enzymes from S.nigrum that converts the starting cholesterol precursorto solasodine aglycone,and the downstreamα-solasonine,α-solamargine,and malonyl-solamargine SGA products.We further identified six enzymes from cultivated eggplant that catalyze the production ofα-solasonine,α-solamargine,and malonyl-solamargine SGAs from solasodine aglycone via glycosylation and atypical malonylation decorations.Our work provides the gene tool box and platform for engineering the production of high-value,steroidal bioactive molecules inheterologoushosts usingsyntheticbiology.

Reprogramming plant specialized metabolism by manipulating protein kinases

Being sessile,plants have evolved sophisticated mechanisms to balance between growth and defense to survive in the harsh environment.The transition from growth to defense is commonly achieved by factors,such as protein kinases(PKs)and transcription factors,that initiate signal transduction and regulate specialized metabolism.Plants produce an array of lineage-specific specialized metabolites for chemical defense and stress tolerance.Some of these molecules are also used by humans as drugs.However,many of these defense-responsive metabolites are toxic to plant cells and inhibitory to growth and development.Plants have,thus,evolved complex regulatory networks to balance the accumulation of the toxic metabolites.Perception of external stimuli is a vital part of the regulatory network.Protein kinase-mediated signaling activates a series of defense responses by phosphorylating the target pro-teins and translating the stimulus into downstream cellular signaling.As biosynthesis of specialized metabolites is triggered when plants perceive stimuli,a possible connection between PKs and spe-cial ized meta bolism is well recognized.However,the roles of PKs in plant specialized metabolism have not received much attention until recently.Here,we summarize the recent advances in understanding PKs in plant specialized metabolism.We aim to highlight how the stimulatory signals are transduced,leading to the biosynthesis of corresponding metabolites.We discuss the post-translational regulation of specialized metabolism and provide insights into the mechanisms by which plants respond to the external signals.In addition,we propose possible strategies to increase the production of plant spe-cial ized metabolites in biotechnological applications using PKs.

Next-Generation Plant Metabolic Engineering, Inspired by an Ancient Chinese Irrigation System

Specialized secondary metabolites serve not only to protect plants against abiotic and biotic challenges, but have also been used extensively by humans to combat diseases. Due to the great importance of medicinal plants for health, we need to find new and sustainable ways to improve the production of the specialized metabolites. In addition to direct extraction, recent progress in metabolic engineering of plants offers an alternative supply option. We argue that metabolic engineering for producing the second- ary metabolites in plants may have distinct advantages over microbial production platforms, and thus pro- pose new approaches of plant metabolic engineering, which are inspired by an ancient Chinese irrigation system. Metabolic engineering strategies work at three levels： introducing biosynthetic genes, using tran- scription factors, and improving metabolic flux including increasing the supply of precursors, energy, and reducing power. In addition, recent progress in biotechnology contributes markedly to better engineering, such as the use of specific promoters and the deletion of competing branch pathways. We propose that next-generation plant metabolic engineering will improve current engineering strategies, for the purpose of producing valuable metabolites in plants on industrial scales.

Occurrence and biosynthesis of plant sesterterpenes (C25), a new addition to terpene diversity

Terpenes,the largest group of plant-specialized metabolites,have received considerable attention for their highly diverse biological activities.Monoterpenes(C10),sesquiterpenes(C15),diterpenes(C20),and triterpenes(C30)have been extensively investigated at both the biochemical and molecular levels over the past two decades.Sesterterpenes(C25),an understudied terpenoid group,were recently described by plant scientists at the molecular level.This review summarizes the plant species that produce sesterterpenes and describes recent developments in the field of sesterterpene biosynthesis,placing a special focus on the catalytic mechanism and evolution of geranylfarnesyl diphosphate synthase and sesterterpene synthase.Finally,we propose several questions to be addressed in future studies,which may help to elucidate sesterterpene metabolism in plants.