Metabolome diversity: too few genes, too many metabolites?

Reliable reference gene selection for quantitative real-time PCR (qRT-PCR) in floral developmental phases of dioecious species Coccinia grandis

The flowering process is intricate and regulated by a combination of external and internal factors. Delving into gene expression research has the potential to enhance our comprehension of the molecular foundations underlying floral development. Because of its accuracy, specificity, reproducibility, and efficiency, qRT-PCR is now a biological research tool for studying expression pattern of desired genes. The gene expression investigations using qRT-PCR required a reference gene with relatively uniform expression levels in multiple biological samples, including different developmental stages, tissues, and experimental conditions. In this study, experimental sets offloral and floral organ development in the male and female plants of C. grandis, a dioecious Cucurbitaceae species, qRT-PCR profiling was performed using six reference genes as internal control with B-class floral identity gene, PISTILLATA (PI). To analyse the data, algorithms such as geNorm, NormFinder, RefFinder, and BestKeeper were used to pick out the best internal controls from a group of candidates. The optimal reference gene for qRT-PCR studies with floral samples has been recommended as β-actin combined with β-tubulin. This is the first report on the validation of candidate reference genes across flower developmental stages in the dioecious species C. grandis, which will provide basic data for research on the molecular mechanism underlying flower development in this species and lay the groundwork for similar studies in other related species.

Metabolomics-centered mining of plant metabolic diversity and function: Past decade and future perspectives

Plants are natural experts in organic synthesis, being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to variable survival challenges. Metabolomics is a research discipline that integrates the capabilities of several types of research including analytical chemistry, statistics, and biochemistry. Its ongoing development provides strategies for gaining a systematic understanding of quantitative changes in the levels of metabolites. Metabolomics is usually performed by targeting either a specific cell, a specific tissue, or the entire organism. Considerable advances in science and technology over the last three decades have propelled us into the era of multi-omics, in which metabolomics, despite at an earlier developmental stage than genomics, transcriptomics, and proteomics, offers the distinct advantage of studying the cellular entities that have the greatest influence on end phenotype. Here, we summarize the state of the art of metabolite detection and identification, and illustrate these techniques with four case study applications: (i) comparing metabolite composition within and between species, (ii) assessing spatio-temporal metabolic changes during plant development, (iii) mining characteristic metabolites of plants in different ecological environments and upon exposure to various stresses, and (iv) assessing the performance of metabolomics as a means of functional gene identification , metabolic pathway elucidation, and metabolomics-assisted breeding through analyzing plant populations with diverse genetic variations. In addition, we highlight the prominent contributions of joint analyses of plant metabolomics and other omics datasets, including those from genomics, transcriptomics, proteomics, epigenomics, phenomics, microbiomes, and ion-omics studies. Finally, we discuss future directions and challenges exploiting metabolomics-centered approaches in understanding plant metabolic diversity.

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.

Central carbon metabolism remodeling as a mechanism to develop drug tolerance and drug resistance in Mycobacterium tuberculosis

Suboptimal efficacy of the current antibiotic regimens and frequent emergence of antibiotic-resistant Mycobacterium tuberculosis (Mtb), an etiological agent of tuberculosis (TB), render TB the world’s deadliest infectious disease before the COVID-19 outbreak. Our outdated TB treatment method is designed to eradicate actively replicating populations of Mtb. Unfortunately, accumulating evidence suggests that a small population of Mtb can survive antimycobacterial pressure of antibiotics by entering a “persister” state (slowly replicating or non-replicating and lacking a stably heritable antibiotic resistance, termed drug tolerance). The formation of drug-tolerant Mtb persisters is associated with TB treatment failure and is thought to be an adaptive strategy for eventual development of permanent genetic mutation-mediated drug resistance. Thus, the molecular mechanisms behind persister formation and drug tolerance acquisition are a source of new antibiotic targets to eradicate both Mtb persisters and drug-resistant Mtb. As Mtb persisters are genetically identical to antibiotic susceptible populations, metabolomics has emerged as a vital biochemical tool to differentiate these populations by determining phenotypic shifts and metabolic reprogramming. Metabolomics, which provides detailed insights into the molecular basis of drug tolerance and resistance in Mtb, has unique advantages over other techniques by its ability to identify specific metabolic differences between the two genetically identical populations. This review summarizes the recent advances in our understanding of the metabolic adaptations used by Mtb persisters to achieve intrinsic drug tolerance and facilitate the emergence of drug resistance. These findings present metabolomics as a powerful tool to identify previously unexplored antibiotic targets and improved combinations of drug regimens against drug-resistant TB infection.

Genome-Wide Association Study With Growth-Related Traits and Secondary Metabolite Contents in Red- and White-Heart Chinese Fir

Chinese fir [Cunninghamia lanceolata (Lamb.) Hook] is an important evergreen coniferous tree species that is widely distributed in many southern provinces of China and has important economic value. The Chinese fir accounts for 1/4 and 1/3 of the total artificial forest area and stock volume, respectively. Red-heart Chinese fir is popular in the market because of its high density and red heartwood. The long-growth cycle hindered the breeding process of Chinese fir, while molecular marker-assisted breeding could accelerate it. However, Chinese fir, a perennial conifer species, has a large genome, which has not yet been published. In this study, the growth-related traits and secondary metabolite contents of red- and white-heart Chinese fir were measured and found to be different between them. There are extremely significant differences among growth-related traits (p < 0.001), but secondary metabolite contents have different correlations due to differences in chemical structure. Moreover, genotype effect analysis of the substantially correlated single nucleotide polymorphisms (SNPs) revealed that most of the loci related to each growth-related traits were different from each other, indicating a type specificity of the genes regulated different growth-related traits. Furthermore, among the loci related to secondary metabolite contents, nine loci associated with multiple metabolite phenotypes such as Marker21022_4, Marker21022_172, Marker24559_31, Marker27425_37, Marker20748_85, Marker18841_115, Marker18841_198, Marker65846_146, and Marker21486_163, suggesting the presence of pleiotropic genes. This study identified the potential SNP markers associated with secondary metabolites in Chinese fir, thus setting the basis for molecular marker-assisted selection.

Methods for Root Exudate Collection and Analysis

Plant root exudation has long been recognized as a vital communication system between plants and microbial communities populating the rhizosphere. Due to the high complexity of the collection process and analysis, a variety of techniques have been developed to mimic natural exudation conditions. In addition, significant progress improving existing techniques and developing new methodologies of root exudate collection and analysis have been made. However, optimal standard methods that compare closely with environmental soil conditions are not yet available. In this review, we provide an overview of all those topics and provide suggestions for improvement.

Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks

Over the last decade, a giant leap forward has been made in resolving the main bottleneck in metabolomics, i.e., the structural characterization of the many unknowns. This has led to the next challenge in this research field: retrieving biochemical pathway information from the various types of networks that can be constructed from metabolome data. Searching putative biochemical pathways, referred to as biotransformation paths, is complicated because several flaws occur during the construction of metabolome networks. Multiple network analysis tools have been developed to deal with these flaws, while in silico retrosynthesis is appearing as an alternative approach. In this review, the different types of metabolome networks, their flaws, and the various tools to trace these biotransformation paths are discussed.

Metabolite-based genome-wide association study enables dissection of the flavonoid decoration pathway of wheat kernels

The marriage of metabolomic approaches with genetic design has proven a powerful tool in dissecting diversity in the metabolome and has additionally enhanced our understanding of complex traits. That said, such studies have rarely been carried out in wheat. In this study, we detected 805 metabolites from wheat kernels and profiled their relative contents among 182 wheat accessions, conducting a metabolite-based genome-wide association study (mGWAS) utilizing 14 646 previously described polymorphic SNP markers. A total of 1098 mGWAS associations were detected with large effects, within which 26 candidate genes were tentatively designated for 42 loci. Enzymatic assay of two candidates indicated they could catalyse glucosylation and subsequent malonylation of various flavonoids and thereby the major flavonoid decoration pathway of wheat kernel was dissected. Moreover, numerous high-confidence genes associated with metabolite contents have been provided, as well as more subdivided metabolite networks which are yet to be explored within our data. These combined efforts presented the first step towards realizing metabolomics-associated breeding of wheat.

Age-Dependent Metabolic Profiles Unravel the Metabolic Relationships Within and Between Flax Leaves (Linum usitatissimum)

Flax for oil seed is a crop of increasing popularity, but its cultivation needs technical improvement. Important agronomic traits such as productivity and resistance to stresses are to be regarded as the result of the combined responses of individual organs and their inter-communication. Ultimately, these responses directly reflect the metabolic profile at the cellular level. Above ground, the complexity of the plant phenotype is governed by leaves at different developmental stages, and their ability to synthesise and exchange metabolites. In this study, the metabolic profile of differently-developed leaves was used firstly to discriminate flax leaf developmental stages, and secondly to analyse the allocation of the metabolites within and between leaves. For this purpose, the concentration of 52 metabolites, both primary and specialized, was followed by gas chromatography (GC-) and liquid chromatography coupled to mass spectrometry (LC-MS) in alternate pairs of flax leaves. On the basis of their metabolic content, three populations of leaves in different growth stages could be distinguished. Primary and specialized metabolites showed characteristic distribution patterns, and compounds similarly evolving with leaf age could be grouped by the aid of the Kohonen self-organising map (SOM) algorithm. Ultimately, visualisation of the correlations between metabolites via hierarchical cluster analysis (HCA) allowed the assessment of the metabolic fluxes characterising different leaf developmental stages, and the investigation of the relationships between primary and specialized metabolites.

Chemical Discovery in the Era of Metabolomics

Untargeted metabolomics aims to quantify the complete set of metabolites within a biological system, most commonly by liquid chromatography/mass spectrometry (LC/MS). Since nearly the inception of the field, compound identification has been widely recognized as the rate-limiting step of the experimental workflow. In spite of exponential increases in the size of metabolomic databases, which now contain experimental MS/MS spectra for over a half a million reference compounds, chemical structures still cannot be confidently assigned to many signals in a typical LC/MS dataset. The purpose of this Perspective is to consider why identification rates continue to be low in untargeted metabolomics. One rationalization is that many naturally occurring metabolites detected by LC/MS are true "novel" compounds that have yet to be incorporated into metabolomic databases. An alternative possibility, however, is that research data do not provide database matches because of informatic artifacts, chemical contaminants, and signal redundancies. Increasing evidence suggests that, for at least some sample types, many unidentifiable signals in untargeted metabolomics result from the latter rather than new compounds originating from the specimen being measured. The implications of these observations on chemical discovery in untargeted metabolomics are discussed.

Metabolic diversification of nitrogen-containing metabolites by the expression of a heterologous lysine decarboxylase gene in Arabidopsis

Lysine decarboxylase converts l-lysine to cadaverine as a branching point for the biosynthesis of plant Lys-derived alkaloids. Although cadaverine contributes towards the biosynthesis of Lys-derived alkaloids, its catabolism, including metabolic intermediates and the enzymes involved, is not known. Here, we generated transgenic Arabidopsis lines by expressing an exogenous lysine/ornithine decarboxylase gene from Lupinus angustifolius (La-L/ODC) and identified cadaverine-derived metabolites as the products of the emerged biosynthetic pathway. Through untargeted metabolic profiling, we observed the upregulation of polyamine metabolism, phenylpropanoid biosynthesis and the biosynthesis of several Lys-derived alkaloids in the transgenic lines. Moreover, we found several cadaverine-derived metabolites specifically detected in the transgenic lines compared with the non-transformed control. Among these, three specific metabolites were identified and confirmed as 5-aminopentanal, 5-aminopentanoate and δ-valerolactam. Cadaverine catabolism in a representative transgenic line (DC29) was traced by feeding stable isotope-labeled [α-¹⁵ N]- or [ε-¹⁵ N]-l-lysine. Our results show similar ¹⁵ N incorporation ratios from both isotopomers for the specific metabolite features identified, indicating that these metabolites were synthesized via the symmetric structure of cadaverine. We propose biosynthetic pathways for the metabolites on the basis of metabolite chemistry and enzymes known or identified through catalyzing specific biochemical reactions in this study. Our study shows that this pool of enzymes with promiscuous activities is the driving force for metabolite diversification in plants. Thus, this study not only provides valuable information for understanding the catabolic mechanism of cadaverine but also demonstrates that cadaverine accumulation is one of the factors to expand plant chemodiversity, which may lead to the emergence of Lys-derived alkaloid biosynthesis.

Exploiting enzyme promiscuity to shape plant specialized metabolism

The amazing variability of plant metabolism and its rapid divergence during evolution pose fundamental questions as to the driving forces, mechanisms, and players in metabolic differentiation. This review examines concepts that help us understand adaptive pathway evolution, with a particular emphasis on plant specialized metabolism, previously often termed secondary metabolism. Following a general introduction to pathway and metabolite evolution, the focus is directed to enzyme promiscuity and its classification. Promiscuous enzymes (or substrates), 'silent' elements of the metabolome, and the 'underground metabolism' may be used and combined to evolve 'new' metabolic pathways. It appears that new pathways rarely appear from scratch, but instead emerge from 'floppy' enzymes and elements of a 'messy' metabolism, and in this way a range of metabolites is generated, some of which may provide benefits to the plant.

Can Herbivore-Induced Volatiles Protect Plants by Increasing the Herbivores' Susceptibility to Natural Pathogens?

In response to insect herbivory, plants mobilize various defenses. Defense responses include the release of herbivore-induced plant volatiles (HIPVs) that can serve as signals to alert undamaged tissues and to attract natural enemies of the herbivores. Some HIPVs can have a direct negative impact on herbivore survival, but it is not well understood by what mechanisms. Here, we tested the hypothesis that exposure to HIPVs renders insects more susceptible to natural pathogens. Exposure of the caterpillars of the noctuid Spodoptera exigua to indole and linalool, but not exposure to (Z)-3-hexenyl acetate, increased the susceptibility to Spodoptera exigua multiple nucleopolyhedrovirus (SeMNPV). We also found that exposure to indole, but not exposure to linalool or (Z)-3-hexenyl acetate, increased the pathogenicity of Bacillus thuringiensis Additional experiments revealed significant changes in microbiota composition after forty-eight hours of larval exposure to indole. Overall, these results provide evidence that certain HIPVs can strongly enhance the susceptibility of caterpillars to pathogens, possibly through effects on the insect gut microbiota. These findings suggest a novel mechanism by which HIPVs can protect plants from herbivorous insects.IMPORTANCE Multitrophic interactions involving insect pests, their natural enemies, microorganisms, and plant hosts are increasingly being recognized as relevant factors in pest management. In response to herbivory attacks, plants activate a wide range of defenses that aim to mitigate the damage. Attacked plants release herbivore-induced plant volatiles (HIPVs), which can act as priming signals for other plants and attract natural enemies of herbivores, and which may have a direct negative impact on herbivore survival. In the present work, we show that exposure of the insects to the induced volatiles could increase the insects' susceptibility to the entomopathogens naturally occurring in the plant environment. These findings suggest a novel role for plant volatiles by influencing insect interactions with natural pathogens, probably mediated by alterations in the insect microbiota composition. In addition, this work provides evidence for selectable plant traits (production of secondary metabolites) that can have an influence on the ecology of the pests and could be relevant in the improvement of pest management strategies using natural entomopathogens.

Genome-Wide Association Studies of Free Amino Acid Levels by Six Multi-Locus Models in Bread Wheat

Genome-wide association studies (GWAS) have been widely used to dissect the complex biosynthetic processes of plant metabolome. Most studies have used single-locus GWAS approaches, such as mixed linear model (MLM), and little is known about more efficient algorithms to implement multi-locus GWAS. Here, we report a comprehensive GWAS of 20 free amino acid (FAA) levels in kernels of bread wheat (Triticumaestivum L.) based on 14,646 SNPs by six multi-locus models (FASTmrEMMA, FASTmrMLM, ISISEM-BLASSO, mrMLM, pKWmEB, and pLARmEB). Our results showed that 328 significant quantitative trait nucleotides (QTNs) were identified in total (38, 8, 92, 45, 117, and 28, respectively, for the above six models). Among them, 66 were repeatedly detected by more than two models, and 155 QTNs appeared only in one model, indicating the reliability and complementarity of these models. We also found that the number of significant QTNs for different FAAs varied from 8 to 41, which revealed the complexity of the genetic regulation of metabolism, and further demonstrated the necessity of the multi-locus GWAS. Around these significant QTNs, 15 candidate genes were found to be involved in FAA biosynthesis, and one candidate gene (TraesCS1D01G052500, annotated as tryptophan decarboxylase) was functionally identified to influence the content of tryptamine in vitro. Our study demonstrated the power and efficiency of multi-locus GWAS models in crop metabolome research and provided new insights into understanding FAA biosynthesis in wheat.

Global analysis of threonine metabolism genes unravel key players in rice to improve the abiotic stress tolerance

The diversity in plant metabolites with improved phytonutrients is essential to achieve global food security and sustainable crop yield. Our study using computational metabolomics genome wide association study (cmGWAS) reports on a comprehensive profiling of threonine (Thr) metabolite in rice. Sixteen abiotic stress responsive (AbSR) – Thr metabolite producing genes (ThrMPG), modulate metabolite levels and play a significant role determining both physiological and nutritional importance of rice. These AbSR-ThrMPG were computationally analysed for their protein properties using OryzaCyc through plant metabolic network analyser. A total of 1373 and 1028 SNPs were involved in complex traits and genomic variations. Comparative mapping of AbSR-ThrMPG revealed the chromosomal colinearity with C4 grass species. Further, computational expression pattern of these genes predicted a differential expression profiling in diverse developmental tissues. Protein interaction of protein coding gene sequences revealed that the abiotic stresses (AbS) are multigenic in nature. In silico expression of AbSR-ThrMPG determined the putative involvement in response to individual AbS. This is the first comprehensive genome wide study reporting on AbSR –ThrMPG analysis in rice. The results of this study provide a pivotal resource for further functional investigation of these key genes in the vital areas of manipulating AbS signaling in rice improvement.

Handling Complexity in Animal and Plant Science Research-From Single to Functional Traits: Are We There Yet?

The current knowledge of the main factors governing livestock, crop and plant quality as well as yield in different species is incomplete. For example, this can be evidenced by the persistence of benchmark crop varieties for many decades in spite of the gains achieved over the same period. In recent years, it has been demonstrated that molecular breeding based on DNA markers has led to advances in breeding (animal and crops). However, these advances are not in the way that it was anticipated initially by the researcher in the field. According to several scientists, one of the main reasons for this was related to the evidence that complex target traits such as grain yield, composition or nutritional quality depend on multiple factors in addition to genetics. Therefore, some questions need to be asked: are the current approaches in molecular genetics the most appropriate to deal with complex traits such as yield or quality? Are the current tools for phenotyping complex traits enough to differentiate among genotypes? Do we need to change the way that data is collected and analysed?

Transcriptomic and metabolic flux analyses reveal shift of metabolic patterns during rice grain development

BACKGROUND

Rice (Oryza sativa) is one of the most important grain crops, which serves as food source for nearly half of the world population. The study of rice development process as well as related strategies for production has made significant progress. However, the comprehensive study on development of different rice tissues at both transcriptomic and metabolic flux level across different stages was lacked.

RESULTS

In this study, we performed RNA-Seq and characterized the expression profiles of differentiated tissues from Oryza sativa Zhonghua 11, including leaves, sheath, stamen, pistil, lemma and palea of the booting stage, and embryo, endosperm, lemma and palea of the mature grain stage. By integrating this set of transcriptome data of different rice tissues at different stages with a genome-scale rice metabolic model, we generated tissue-specific models and investigated the shift of metabolic patterns, and the discrepancy between transcriptomic and metabolic level. We found although the flux patterns are not very similar with the gene expression pattern, the tissues at booting stage and mature grain stage can be separately clustered by primary metabolism at either level. While the gene expression and flux distribution of secondary metabolism is more diverse across tissues and stages. The critical rate-limiting reactions and pathways were also identified. In addition, we compared the patterns of the same tissue at different stages and the different tissues at same stage. There are more altered pathways at gene expression level than metabolic level, which indicate the metabolism is more robust to reflect the phenotype, and might largely because of the complex post-transcriptional modification.

CONCLUSIONS

The tissue-specific models revealed more detail metabolic pattern shift among different tissues and stages, which is of great significance to uncover mechanism of rice grain development and further improve production and quality of rice.

Functional evolution of biosynthetic enzymes that produce plant volatiles

Plants synthesize volatile compounds to attract pollinators. The volatiles emitted by flowers are often complex mixtures of organic compounds; pollinators are capable of distinctly recognizing different volatile compounds. Plants also produce volatile compounds to protect themselves against herbivores and pathogens. Some of the volatile compounds produced in floral and vegetative tissues are toxic to insects and microbes. To adapt changes in the environment, plants have evolved the ability to synthesize a unique set of volatiles. Intensive studies have identified and characterized the enzymes responsible for the formation of plant volatiles. In particular, many biosynthetic genes have been isolated and their enzymatic functions have been proposed. This review describes how plants have evolved the biosynthetic pathways leading to the formation of green leaf volatiles and phenylpropene volatiles.

Volatile Compound and Gene Expression Analyses Reveal Temporal and Spatial Production of LOX-Derived Volatiles in Pepino (Solanum muricatum Aiton) Fruit and LOX Specificity

Lipoxygenase (LOX) is an important contributor to aroma compounds in most fresh produce; however, little is known about the LOX pathway in pepino (Solanum muricatum Aiton) fruit. We explored the LOX aroma compounds produced by the flesh and the peel and identified eight putative LOX genes expressed in both tissues during fruit growth and development during two consecutive seasons. This study shows that pepino produces C5, C6, and C9 LOX-derived compounds. Odorant C9 volatiles were produced during immature stages with a concomitant decrease when the fruit ripens, whereas C5 and C6 compounds were formed throughout ripening. trans-2-Hexenal and its alcohol were produced in the peel, but not detected in the flesh. The expression of three genes, SmLOXD (putative 13-LOX), SmLOXB, and SmLOX5-like1 (putative 9-LOXs), increased during fruit ripening. These genes may account for aroma volatiles in pepino. Here, we discuss the possible roles of individual LOX genes in pepino.

Characterization of poplar metabotypes via mass difference enrichment analysis

Instrumentation technology for metabolomics has advanced drastically in recent years in terms of sensitivity and specificity. Despite these technical advances, data analytical strategies are still in their infancy in comparison with other 'omics'. Plants are known to possess an immense diversity of secondary metabolites. Typically, more than 70% of metabolomics data are not amenable to systems biological interpretation because of poor database coverage. Here, we propose a new general strategy for mass-spectrometry-based metabolomics that incorporates all exact mass features with known sum formulas into the evaluation and interpretation of metabolomics studies. We extend the use of mass differences, commonly used for feature annotation, by redefining them as variables that reflect the remaining 'omic' domains. The strategy uses exact mass difference network analyses exemplified for the metabolomic description of two grey poplar (Populus × canescens) genotypes that differ in their capability to emit isoprene. This strategy established a direct connection between the metabotype and the non-isoprene-emitting phenotype, as mass differences pertaining to prenylation reactions were over-represented in non-isoprene-emitting poplars. Not only was the analysis of mass differences able to grasp the known chemical biology of poplar, but it also improved the interpretability of yet unknown biochemical relationships.

Drawing Links from Transcriptome to Metabolites: The Evolution of Aroma in the Ripening Berry of Moscato Bianco (Vitis vinifera L.)

Monoterpenes confer typical floral notes to "Muscat" grapevine varieties and, to a lesser extent, to other aromatic non-Muscat varieties. Previous studies have led to the identification and functional characterization of some enzymes and genes in this pathway. However, the underlying genetic map is still far from being complete. For example, the specific steps of monoterpene metabolism and its regulation are largely unknown. With the aim of identifying new candidates for the missing links, we applied an integrative functional genomics approach based on the targeted metabolic and genome-wide transcript profiling of Moscato Bianco ripening berries. In particular, gas chromatography-mass spectrometry analysis of free and bound terpenoid compounds was combined with microarray analysis in the skins of berries collected at five developmental stages from pre-veraison to over-ripening. Differentially expressed metabolites and probes were identified in the pairwise comparison between time points by using the early stage as a reference. Metabolic and transcriptomic data were integrated through pairwise correlation and clustering approaches to discover genes linked with particular metabolites or groups of metabolites. These candidate transcripts were further checked for co-localization with quantitative trait loci (QTLs) affecting aromatic compounds. Our findings provide insights into the biological networks of grapevine secondary metabolism, both at the catalytic and regulatory levels. Examples include a nudix hydrolase as component of a terpene synthase-independent pathway for monoterpene biosynthesis, genes potentially involved in monoterpene metabolism (cytochrome P450 hydroxylases, epoxide hydrolases, glucosyltransferases), transport (vesicle-associated proteins, ABCG transporters, glutathione S-transferases, amino acid permeases), and transcriptional control (transcription factors of the ERF, MYB and NAC families, intermediates in light- and circadian cycle-mediated regulation with supporting evidence from the literature and additional regulatory genes with a previously unreported association to monoterpene accumulation).

GC-MS Metabolomic Analysis to Reveal the Metabolites and Biological Pathways Involved in the Developmental Stages and Tissue Response of Panax ginseng

Ginsenosides, the major compounds present in ginseng, are known to have numerous physiological and pharmacological effects. The physiological processes, enzymes and genes involved in ginsenoside synthesis in P. ginseng have been well characterized. However, relatively little information is known about the dynamic metabolic changes that occur during ginsenoside accumulation in ginseng. To explore this topic, we isolated metabolites from different tissues at different growth stages, and identified and characterized them by using gas chromatography coupled with mass spectrometry (GC-MS). The results showed that a total of 30, 16, 20, 36 and 31 metabolites were identified and involved in different developmental stages in leaf, stem, petiole, lateral root and main root, respectively. To investigate the contribution of tissue to the biosynthesis of ginsenosides, we examined the metabolic changes of leaf, stem, petiole, lateral root and main root during five development stages: 1-, 2-, 3-, 4- and 5-years. The score plots of partial least squares-discriminate analysis (PLS-DA) showed clear discrimination between growth stages and tissue samples. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis in the same tissue at different growth stages indicated profound biochemical changes in several pathways, including carbohydrate metabolism and pentose phosphate metabolism, in addition, the tissues displayed significant variations in amino acid metabolism, sugar metabolism and energy metabolism. These results should facilitate further dissection of the metabolic flux regulation of ginsenoside accumulation in different developmental stages or different tissues of ginseng.

Monoterpene 'thermometer' of tropical forest-atmosphere response to climate warming

Tropical forests absorb large amounts of atmospheric CO₂ through photosynthesis but elevated temperatures suppress this absorption and promote monoterpene emissions. Using ¹³ CO₂ labeling, here we show that monoterpene emissions from tropical leaves derive from recent photosynthesis and demonstrate distinct temperature optima for five groups (Groups 1-5), potentially corresponding to different enzymatic temperature-dependent reaction mechanisms within β-ocimene synthases. As diurnal and seasonal leaf temperatures increased during the Amazonian 2015 El Niño event, leaf and landscape monoterpene emissions showed strong linear enrichments of β-ocimenes (+4.4% °C^-1 ) at the expense of other monoterpene isomers. The observed inverse temperature response of α-pinene (-0.8% °C^-1 ), typically assumed to be the dominant monoterpene with moderate reactivity, was not accurately simulated by current global emission models. Given that β-ocimenes are highly reactive with respect to both atmospheric and biological oxidants, the results suggest that highly reactive β-ocimenes may play important roles in the thermotolerance of photosynthesis by functioning as effective antioxidants within plants and as efficient atmospheric precursors of secondary organic aerosols. Thus, monoterpene composition may represent a new sensitive 'thermometer' of leaf oxidative stress and atmospheric reactivity, and therefore a new tool in future studies of warming impacts on tropical biosphere-atmosphere carbon-cycle feedbacks.

Metabolomics-guided analysis of isocoumarin production by Streptomyces species MBT76 and biotransformation of flavonoids and phenylpropanoids

INTRODUCTION

Actinomycetes produce the majority of the antibiotics currently in clinical use. The efficiency of antibiotic production is affected by multiple factors such as nutrients, pH, temperature and growth phase. Finding the optimal harvesting time is crucial for successful isolation of the desired bioactive metabolites from actinomycetes, but for this conventional chemical analysis has limitations due to the metabolic complexity.

OBJECTIVES

This study explores the utility of NMR-based metabolomics for (1) optimizing fermentation time for the production of known and/or unknown bioactive compounds produced by actinomycetes; (2) elucidating the biosynthetic pathway for microbial natural products; and (3) facilitating the biotransformation of nature-abundant chemicals.

METHOD

The aqueous culture broth of actinomycete Streptomyces sp. MBT76 was harvested every 24 h for 5 days and each broth was extracted by ethyl acetate. The extracts were analyzed by ¹H NMR spectroscopy and the data were compared with principal component analysis (PCA) and orthogonal projection to latent structures (OPLS) analysis. Antimicrobial test were performed by agar diffusion assay.

RESULTS

The secondary metabolites production by Streptomyces sp. MBT76 was growth phase-dependent. Isocoumarins (1-9), undecylprodiginine (10), streptorubin B (11), 1H-pyrrole-2-carboxamide (12), acetyltryptamine (13), and fervenulin (14) were identified, and their optimal production time was determined in crude extracts without tedious chromatographic fractionation. Of these compounds, 5,6,7,8-tetramethoxyl-3-methyl-isocoumarin (9) is as a novel compound, which was most likely synthesized by a type I iterative polyketide synthase (PKS) encoded by the icm gene cluster. Multivariate data analysis of the ¹H NMR spectra showed that acetyltryptamine (13) and tri-methoxylated isocoumarins (7 and 8) were the major determinants of antibiotic activity during later time points. The methoxylation was exploited to allow bioconversion of exogenously added genistein into a suite of methoxylated isoflavones (15-18). Methoxylation increased the antimicrobial efficacy of isocoumarins, but decreased that of the isoflavones.

CONCLUSION

Our results show the applicability of NMR-based metabolic profiling to streamline microbial biotransformation and to determine the optimal harvesting time of actinomycetes for antibiotic production.

Evolutionary Rate Heterogeneity of Primary and Secondary Metabolic Pathway Genes in Arabidopsis thaliana

Primary metabolism is essential to plants for growth and development, and secondary metabolism helps plants to interact with the environment. Many plant metabolites are industrially important. These metabolites are produced by plants through complex metabolic pathways. Lack of knowledge about these pathways is hindering the successful breeding practices for these metabolites. For a better knowledge of the metabolism in plants as a whole, evolutionary rate variation of primary and secondary metabolic pathway genes is a prerequisite. In this study, evolutionary rate variation of primary and secondary metabolic pathway genes has been analyzed in the model plant Arabidopsis thaliana. Primary metabolic pathway genes were found to be more conserved than secondary metabolic pathway genes. Several factors such as gene structure, expression level, tissue specificity, multifunctionality, and domain number are the key factors behind this evolutionary rate variation. This study will help to better understand the evolutionary dynamics of plant metabolism.

Metabolic profiling as a tool for prioritizing antimicrobial compounds

Metabolomics is an analytical technique that allows scientists to globally profile low molecular weight metabolites between samples in a medium- or high-throughput environment. Different biological samples are statistically analyzed and correlated to a bioactivity of interest, highlighting differentially produced compounds as potential biomarkers. Here, we review NMR- and MS-based metabolomics as technologies to facilitate the identification of novel antimicrobial natural products from microbial sources. Approaches to elicit the production of poorly expressed (cryptic) molecules are thereby a key to allow statistical analysis of samples to identify bioactive markers, while connection of compounds to their biosynthetic gene cluster is a determining step in elucidating the biosynthetic pathway and allows downstream process optimization and upscaling. The review focuses on approaches built around NMR-based metabolomics, which enables efficient dereplication and guided fractionation of (antimicrobial) compounds.

Molecular cloning of melatonin 2-hydroxylase responsible for 2-hydroxymelatonin production in rice (Oryza sativa)

Although melatonin biosynthetic genes from plants have been cloned, the melatonin catabolism mechanisms remain unclear. To clone the genes responsible for melatonin metabolism, we ectopically expressed 35 full-length cDNAs of rice 2-oxoglutarate-dependent dioxygenase (2-ODD) in Escherichia coli and purified the corresponding recombinant proteins. In vitro 2-ODD assays showed four independent 2-ODD proteins that were able to catalyze melatonin into 2-hydroxymelatonin, exhibiting melatonin 2-hydroxylase (M2H). These M2H proteins had peak activities at pH 8.0 and 30°C. The Km ranged from 121 μm to 371 μm with the Vmax ranging from 1.7 to 18.5 pkat/mg protein, respectively. The M2H enzyme activities were dependent on cofactors such as α-ketoglutarate, ascorbate, and Fe(2+), similar to the 2-ODD enzymes. M2H activity was inhibited by prohexadione-Ca, an inhibitor of 2-ODD, in a dose-dependent manner. M2H activity was high in the roots of rice seedlings, concurrent with high transcription levels of 2-ODD 21, suggesting that 2-ODD 21 was a major gene for M2H activity. Analogous to the high M2H activity in the roots, 2-hydroxymelatonin was found in large quantities in roots treated with melatonin. These results suggest that melatonin was metabolized into 2-hydroxymelatonin by the M2H genes in plants, but the physiological significance of 2-hydroxymelatonin remains to be examined in the future.

Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism

Plants produce structurally diverse secondary (specialized) metabolites to increase their fitness for survival under adverse environments. Several bioactive compounds for new drugs have been identified through screening of plant extracts. In this study, genome-wide association studies (GWAS) were conducted to investigate the genetic architecture behind the natural variation of rice secondary metabolites. GWAS using the metabolome data of 175 rice accessions successfully identified 323 associations among 143 single nucleotide polymorphisms (SNPs) and 89 metabolites. The data analysis highlighted that levels of many metabolites are tightly associated with a small number of strong quantitative trait loci (QTLs). The tight association may be a mechanism generating strains with distinct metabolic composition through the crossing of two different strains. The results indicate that one plant species produces more diverse phytochemicals than previously expected, and plants still contain many useful compounds for human applications.

Biofuel production: an odyssey from metabolic engineering to fermentation scale-up

Metabolic engineering has developed microbial cell factories that can convert renewable carbon sources into biofuels. Current molecular biology tools can efficiently alter enzyme levels to redirect carbon fluxes toward biofuel production, but low product yield and titer in large bioreactors prevent the fulfillment of cheap biofuels. There are three major roadblocks preventing economical biofuel production. First, carbon fluxes from the substrate dissipate into a complex metabolic network. Besides the desired product, microbial hosts direct carbon flux to synthesize biomass, overflow metabolites, and heterologous enzymes. Second, microbial hosts need to oxidize a large portion of the substrate to generate both ATP and NAD(P)H to power biofuel synthesis. High cell maintenance, triggered by the metabolic burdens from genetic modifications, can significantly affect the ATP supply. Thereby, fermentation of advanced biofuels (such as biodiesel and hydrocarbons) often requires aerobic respiration to resolve the ATP shortage. Third, mass transfer limitations in large bioreactors create heterogeneous growth conditions and micro-environmental fluctuations (such as suboptimal O₂ level and pH) that induce metabolic stresses and genetic instability. To overcome these limitations, fermentation engineering should merge with systems metabolic engineering. Modern fermentation engineers need to adopt new metabolic flux analysis tools that integrate kinetics, hydrodynamics, and ¹³C-proteomics, to reveal the dynamic physiologies of the microbial host under large bioreactor conditions. Based on metabolic analyses, fermentation engineers may employ rational pathway modifications, synthetic biology circuits, and bioreactor control algorithms to optimize large-scale biofuel production.

Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism

Plant metabolites are important to world food security in terms of maintaining sustainable yield and providing food with enriched phytonutrients. Here we report comprehensive profiling of 840 metabolites and a further metabolic genome-wide association study based on ∼6.4 million SNPs obtained from 529 diverse accessions of Oryza sativa. We identified hundreds of common variants influencing numerous secondary metabolites with large effects at high resolution. We observed substantial heterogeneity in the natural variation of metabolites and their underlying genetic architectures among different subspecies of rice. Data mining identified 36 candidate genes modulating levels of metabolites that are of potential physiological and nutritional importance. As a proof of concept, we functionally identified or annotated five candidate genes influencing metabolic traits. Our study provides insights into the genetic and biochemical bases of rice metabolome variation and can be used as a powerful complementary tool to classical phenotypic trait mapping for rice improvement.

Application of stable isotope-assisted metabolomics for cell metabolism studies

The applications of stable isotopes in metabolomics have facilitated the study of cell metabolisms. Stable isotope-assisted metabolomics requires: (1) properly designed tracer experiments; (2) stringent sampling and quenching protocols to minimize isotopic alternations; (3) efficient metabolite separations; (4) high resolution mass spectrometry to resolve overlapping peaks and background noises; and (5) data analysis methods and databases to decipher isotopic clusters over a broad m/z range (mass-to-charge ratio). This paper overviews mass spectrometry based techniques for precise determination of metabolites and their isotopologues. It also discusses applications of isotopic approaches to track substrate utilization, identify unknown metabolites and their chemical formulas, measure metabolite concentrations, determine putative metabolic pathways, and investigate microbial community populations and their carbon assimilation patterns. In addition, 13C-metabolite fingerprinting and metabolic models can be integrated to quantify carbon fluxes (enzyme reaction rates). The fluxome, in combination with other "omics" analyses, may give systems-level insights into regulatory mechanisms underlying gene functions. More importantly, 13C-tracer experiments significantly improve the potential of low-resolution gas chromatography-mass spectrometry (GC-MS) for broad-scope metabolism studies. We foresee the isotope-assisted metabolomics to be an indispensable tool in industrial biotechnology, environmental microbiology, and medical research.

Putting bugs to the blush: metabolic engineering for phenylpropanoid-derived products in microorganisms

Phenylpropanoids and phenylpropanoid-derived phenolic compounds such as flavonoids, anthocyanins, or stilbenes are secondary plant metabolites which serve as pigments and scent compounds or provide protection against environmental stress. Due to their antioxidant properties they also have been widely recognized for their benefit on human health. Traditionally, such compounds are extracted from their natural plant sources, but this approach is limited by low abundance and environmental, seasonal as well as regional variations in yield. Chemical synthesis is not a true alternative for the large scale production of more complex phenylpropanoid-derived substances since chemical synthesis becomes commercially unfeasible as the structural complexity of these plant natural products increases. In the last years, many biosynthetic pathways for plant natural products have been elucidated through the advancements in DNA sequencing technologies. In combination with new recombinant DNA technologies this technical progress opens the door toward the functional integration of full biosynthetic pathways for the synthesis of phenylpropanoids and phenylpropanoid-derived compounds in microorganisms. We believe that this approach has great potential to provide sufficient quantities of the desired plant natural product from cheap and renewable resources. This commentary highlights recent advances in the microbial production of phenylpropanoid-derived compounds with an emphasis on flavonoids and stilbenes.

Progress toward single cell metabolomics

The metabolome refers to the entire set of small molecules, or metabolites, within a biological sample. These molecules are involved in many fundamental intracellular functions and reflect the cell's physiological condition. The ability to detect and identify metabolites and determine and monitor their amounts at the single cell level enables an exciting range of studies of biological variation and functional heterogeneity between cells, even within a presumably homogenous cell population. Significant progress has been made in the development and application of bioanalytical tools for single cell metabolomics based on mass spectrometry, microfluidics, and capillary separations. Remarkable improvements in the sensitivity, specificity, and throughput of these approaches enable investigation of multiple metabolites simultaneously in a range of individual cell samples.

Biotransformation of isonitrosoacetophenone (2-keto-2-phenyl-acetaldoxime) in tobacco cell suspensions

Nicotiana tabacum cell suspensions, 2 g wet wt/ml, rapidly took up 1 mM isonitrosoacetophenone (INAP), a plant-derived stress metabolite with anti-oxidative and anti-fungal properties, producing 4'-hexopyranosyloxy-3'-methoxyisonitrosoacetophenone in 54 % yield over 18 h. Unconverted INAP was at 33 μM. UPLC-MS/MS analyses with MassFragment software were used for metabolite identification. INAP had been hydroxylated at its meta- and para-positions as well as undergoing subsequent methoxylation and glycosylation. INAP is thus recognized by the enzymatic machinery of the phenylpropanoid pathway and is converted to a molecule with a substitution pattern similar to ferulic acid.

Patterns of gene and metabolite define the effects of extracellular osmolality on kidney collecting duct

To investigate the effects of changes in extracellular osmolality on the function of kidney collecting duct cells, particularly on water and sodium reabsorption in the conditions of diuresis and antidiuresis, we generated transcriptome and metabolome profiles of primary cultured inner medullary collecting duct (IMCD) cells. They were grown in hyperosmolar culture medium (640 mOsm) for 4 days and then exposed to either reduced (300 mOsm) or same osmolality for 1 or 2 days more. Integrated analysis of the transcriptome and metabolome revealed that decreased extracellular osmolality was associated with decreased levels of organic osmolytes, glucose, intermediates of citric acid cycle, and branched-chain amino acids (BCAA) in IMCD cells, along with significantly decreased gene expression and protein abundance of P-type transporters (ATP1B1), ABC transporters (ABCC5 and ABCG1), and insulin signaling pathways (IRS2). Quantitative real-time RT-PCR and semiquantitative immunoblotting confirmed the changes of transcript levels of differentially expressed genes and protein levels. Taken together, integrated analysis of omics data demonstrated that water and sodium reabsorption could be reduced by decreased extracellular osmolality per se, through decreased levels of ABC transporters and IRS2, which play a potential role in the transport of organic osmolytes, BCAA, glucose, and trafficking of epithelial sodium channel.

Metabolic engineering of microorganisms for the synthesis of plant natural products

Of more than 200,000 plant natural products known to date, many demonstrate important pharmacological activities or are of biotechnological significance. However, isolation from natural sources is usually limited by low abundance and environmental, seasonal as well as regional variation, whereas total chemical synthesis is typically commercially unfeasible considering the complex structures of most plant natural products. With advances in DNA sequencing and recombinant DNA technology many of the biosynthetic pathways responsible for the production of these valuable compounds have been elucidated, offering the opportunity of a functional integration of biosynthetic pathways in suitable microorganisms. This approach offers promise to provide sufficient quantities of the desired plant natural products from inexpensive renewable resources. This review covers recent advancements in the metabolic engineering of microorganisms for the production of plant natural products such as isoprenoids, phenylpropanoids and alkaloids, and highlights general approaches and strategies to gain access to the rich biochemical diversity of plants by employing the biosynthetic power of microorganisms.

The fruit ripening-related gene FaAAT2 encodes an acyl transferase involved in strawberry aroma biogenesis

Short-chain esters contribute to the blend of volatiles that define the strawberry aroma. The last step in their biosynthesis involves an alcohol acyltransferase that catalyses the esterification of an acyl moiety of acyl-CoA with an alcohol. This study identified a novel strawberry alcohol acyltransferase gene (FaAAT2) whose expression pattern during fruit receptacle growth and ripening is in accordance with the production of esters throughout strawberry fruit ripening. The full-length FaAAT2 cDNA was cloned and expressed in Escherichia coli and its activity was analysed with acyl-CoA and alcohol substrates. The semi-purified FaAAT2 enzyme had activity with C1-C8 straight-chain alcohols and aromatic alcohols in the presence of acetyl-CoA. Cinnamyl alcohol was the most efficient acyl acceptor. When FaAAT2 expression was transiently downregulated in the fruit receptacle by agroinfiltration, the volatile ester production was significantly reduced in strawberry fruit. The results suggest that FaAAT2 plays a significant role in the production of esters that contribute to the final strawberry fruit flavour.

A 2-oxoglutarate-dependent dioxygenase from Ruta graveolens L. exhibits p-coumaroyl CoA 2'-hydroxylase activity (C2'H): a missing step in the synthesis of umbelliferone in plants

Coumarins are important compounds that contribute to the adaptation of plants to biotic or abiotic stresses. Among coumarins, umbelliferone occupies a pivotal position in the plant phenylpropanoid network. Previous studies indicated that umbelliferone is derived from the ortho-hydroxylation of p-coumaric acid by an unknown biochemical step to yield 2,4-dihydroxycinnamic acid, which then undergoes spontaneous lactonization. Based on a recent report of a gene encoding a 2-oxoglutarate-dependent dioxygenase from Arabidopsis thaliana that exhibited feruloyl CoA 6'-hydroxylase activity (Bourgaud et al., 2006), we combined a bioinformatic approach and a cDNA library screen to identify an orthologous ORF (Genbank accession number JF799117) from Ruta graveolens L. This ORF shares 59% amino acid identity with feruloyl CoA 6'-hydroxylase, was functionally expressed in Escherichia coli, and converted feruloyl CoA into scopoletin and p-coumaroyl CoA into umbelliferone with equal activity. Its bi-functionality was further confirmed in planta: transient expression of JF799117 in Nicotiana benthamiana yielded plants with leaves containing high levels of umbelliferone and scopoletin when compared to control plants, which contained barely detectable traces of these compounds. The expression of JF799117 was also tightly correlated to the amount of umbelliferone that was found in UV-elicited R. graveolens leaves. Therefore, JF799117 encodes a p-coumaroyl CoA 2'-hydroxylase in R. graveolens, which represents a previously uncharacterized step in the synthesis of umbelliferone in plants. Psoralen, which is an important furanocoumarin in R. graveolens, was found to be a competitive inhibitor of the enzyme, and it may exert this effect through negative feedback on the enzyme at an upstream position in the pathway.