•Plants are considered to biosynthesize specialized metabolites to adapt to environmental stresses.•The function of metabolites induced by abiotic stress in vivo is largely unknown.•Integrated ...metabolomics is a powerful approach to reveal their function.
Plants are considered to biosynthesize specialized (traditionally called secondary) metabolites to adapt to environmental stresses such as biotic and abiotic stresses. The majority of specialized metabolites induced by abiotic stress characteristically exhibit antioxidative activity in vitro, but their function in vivo is largely yet to be experimentally confirmed. In this review, we highlight recent advances in the identification of the role of abiotic stress-responsive specialized metabolites with an emphasis on flavonoids. Integrated ‘omics’ analysis, centered on metabolomics with a series of plant resources differing in their flavonoid accumulation, showed experimentally that flavonoids play a major role in antioxidation in vivo. In addition, the results also suggest the role of flavonoids in the vacuole. To obtain more in-depth insights, chemical and biological challenges need to be addressed for the identification of unknown specialized metabolites and their in vivo functions.
Lipids are the major constituents of biological membranes that can sense extracellular conditions. Lipid‐mediated signaling occurs in response to various environmental stresses, such as temperature ...change, salinity, drought and pathogen attack. Lysophospholipid, fatty acid, phosphatidic acid, diacylglycerol, inositol phosphate, oxylipins, sphingolipid, and N–acylethanolamine have all been proposed to function as signaling lipids. Studies on these stress‐inducible lipid species have demonstrated that each lipid class has specific biological relevance, biosynthetic mechanisms and signaling cascades, which activate defense reactions at the transcriptional level. In addition to their roles in signaling, lipids also function as stress mitigators to reduce the intensity of stressors. To mitigate particular stresses, enhanced syntheses of unique lipids that accumulate in trace quantities under normal growth conditions are often observed under stressed conditions. The accumulation of oligogalactolipids and glucuronosyldiacylglycerol has recently been found to mitigate freezing and nutrition‐depletion stresses, respectively, during lipid remodeling. In addition, wax, cutin and suberin, which are not constituents of the lipid bilayer, but are components derived from lipids, contribute to the reduction of drought stress and tissue injury. These features indicate that lipid‐mediated defenses against environmental stress contributes to plant survival.
Summary
Medicinal plants are a rich source of highly diverse specialized metabolites with important pharmacological properties. Until recently, plant biologists were limited in their ability to ...explore the biosynthetic pathways of these metabolites, mainly due to the scarcity of plant genomics resources. However, recent advances in high‐throughput large‐scale analytical methods have enabled plant biologists to discover biosynthetic pathways for important plant‐based medicinal metabolites. The reduced cost of generating omics datasets and the development of computational tools for their analysis and integration have led to the elucidation of biosynthetic pathways of several bioactive metabolites of plant origin. These discoveries have inspired synthetic biology approaches to develop microbial systems to produce bioactive metabolites originating from plants, an alternative sustainable source of medicinally important chemicals. Since the demand for medicinal compounds are increasing with the world's population, understanding the complete biosynthesis of specialized metabolites becomes important to identify or develop reliable sources in the future. Here, we review the contributions of major omics approaches and their integration to our understanding of the biosynthetic pathways of bioactive metabolites. We briefly discuss different approaches for integrating omics datasets to extract biologically relevant knowledge and the application of omics datasets in the construction and reconstruction of metabolic models.
Significance Statement
Medicinal plants produce highly diverse pharmacologically important specialized metabolites, but the absence of genomics resources has limited their exploitation. Here, we review the recent developments of multi‐omics approach that facilitate analysis of specialized metabolism in medicinal plants.
Shine-Dalgarno (SD) motifs are thought to play an important role in translational initiation in bacteria. Paradoxically, ribosome profiling studies in
show no correlation between the strength of an ...mRNA's SD motif and how efficiently it is translated. Performing profiling on ribosomes with altered anti-Shine-Dalgarno sequences, we reveal a genome-wide correlation between SD strength and ribosome occupancy that was previously masked by other contributing factors. Using the antibiotic retapamulin to trap initiation complexes at start codons, we find that the mutant ribosomes select start sites correctly, arguing that start sites are hard-wired for initiation through the action of other mRNA features. We show that A-rich sequences upstream of start codons promote initiation. Taken together, our genome-wide study reveals that SD motifs are not necessary for ribosomes to determine where initiation occurs, though they do affect how efficiently initiation occurs.
Covering: up to 2021
Plants and their associated microbial communities are known to produce millions of metabolites, a majority of which are still not characterized and are speculated to possess ...novel bioactive properties. In addition to their role in plant physiology, these metabolites are also relevant as existing and next-generation medicine candidates. Elucidation of the plant metabolite diversity is thus valuable for the successful exploitation of natural resources for humankind. Herein, we present a comprehensive review on recent metabolomics approaches to illuminate molecular networks in plants, including chemical isolation and enzymatic production as well as the modern metabolomics approaches such as stable isotope labeling, ultrahigh-resolution mass spectrometry, metabolome imaging (spatial metabolomics), single-cell analysis, cheminformatics, and computational mass spectrometry. Mass spectrometry-based strategies to characterize plant metabolomes through metabolite identification and annotation are described in detail. We also highlight the use of phytochemical genomics to mine genes associated with specialized metabolites' biosynthesis. Understanding the metabolic diversity through biotechnological advances is fundamental to elucidate the functions of the plant-derived specialized metabolome.
Plants and their associated microbial communities are known to produce millions of metabolites, a majority of which are still not characterized and will be illuminated by the advance of metabolomics and the informatics techniques.
ABSTRACT
In West Africa, upland rice (Oryza spp.) is typically grown in low‐input production systems under low soil fertility conditions. Genetic improvement may offer a cost‐effective approach to ...improving the productivity rather than approaches that rely solely on external nutrient inputs. In the 1990s, the upland rice breeding program of the West Africa Rice Development Association (now Africa Rice Center AfricaRice) developed New Rice for Africa (NERICA) cultivars. However, recent studies suggest that there is scope for improving on the currently available NERICA cultivars. The objectives of this study are to (i) quantify yield advantage of two cultivars (Aus 257 and IR 74371‐3‐1‐1) which were identified as high‐yielding ones from a wide range of materials, over NERICA 1, and (ii) identify plant characteristics of these two high‐yielding cultivars. Data were compiled from nine on‐station and 23 on‐farm trials in Benin. On average over all the trials, the two cultivars out yielded local check upland NERICA 1. Particularly, their relative yield advantage was higher when NERICA 1 showed low yield. Aus 257 had greater biomass accumulation, harvest index (HI), and uptake of N, P, and K. Greater biomass accumulation was the result of high leaf area index (LAI). Cultivar variation in nutrient‐use efficiency also contributed to high yield, and IR 74371‐3‐1‐1 showed higher nutrient‐use efficiency than NERICA 1 and Aus 257. These results suggest that the use of the two cultivars with greater biomass accumulation, harvest index, nutrient uptake, and use efficiency is critical for improving rice yield.
•Stable isotopes do not have a significant impact on the production of specialized metabolites in organisms, including plants.•Mass spectrometry-based metabolomics using stable isotope labeling can ...effectively determine known and unknown metabolites.•Identification of the unknown metabolites denotes the biosynthetic genes involved in their metabolism.•The newly identified metabolites and genes shed light on the manner in which specialized metabolism has evolved throughout the plant kingdom.
The exact mechanics of specialized metabolism and its importance throughout plant evolution remain mysterious. Specialized metabolites and their corresponding biosynthetic genes are crucial to understand the reason for the prevalence of certain metabolism. Even though mass spectrometry-based metabolomics has enabled us to acquire data about the structural properties of unknown specialized metabolites as well as known metabolites and their corresponding isomers/analogs, extensive analytical approaches are still required. Herein, we review the most advanced analytical approaches using stable isotope labeling that can be used to identify the unknown specialized metabolites.
We report a computational approach (implemented in MS-DIAL 3.0; http://prime.psc.riken.jp/) for metabolite structure characterization using fully
C-labeled and non-labeled plants and LC-MS/MS. Our ...approach facilitates carbon number determination and metabolite classification for unknown molecules. Applying our method to 31 tissues from 12 plant species, we assigned 1,092 structures and 344 formulae to 3,604 carbon-determined metabolite ions, 69 of which were found to represent structures currently not listed in metabolome databases.
PDF
