A robust circadian rhythm of metabolites in Arabidopsis thaliana mutants with enhanced growth characteristics

Molecular Defensive Mechanism of Echinacea purpurea (L.) Moench against PAH Contaminations

The understanding of the molecular defensive mechanism of Echinacea purpurea (L.) Moench against polycyclic aromatic hydrocarbon (PAH) contamination plays a key role in the further improvement of phytoremediation efficiency. Here, the responses of E. purpurea to a defined mixture of phenanthrene (PHE) and pyrene (PYR) at different concentrations or a natural mixture from an oilfield site with a history of several decades were studied based on transcriptomics sequencing and widely targeted metabolomics approaches. The results showed that upon 60-day PAH exposure, the growth of E. purpurea in terms of biomass (p < 0.01) and leaf area per plant (p < 0.05) was negatively correlated with total PAH concentration and significantly reduced at high PAH level. The majority of genes were switched on and metabolites were accumulated after exposure to PHE + PYR, but a larger set of genes (3964) or metabolites (208) showed a response to a natural PAH mixture in E. purpurea. The expression of genes involved in the pathways, such as chlorophyll cycle and degradation, circadian rhythm, jasmonic acid signaling, and starch and sucrose metabolism, was remarkably regulated, enhancing the ability of E. purpurea to adapt to PAH exposure. Tightly associated with transcriptional regulation, metabolites mainly including sugars and secondary metabolites, especially those produced via the phenylpropanoid pathway, such as coumarins, flavonoids, and their derivatives, were increased to fortify the adaptation of E. purpurea to PAH contamination. These results suggest that E. purpurea has a positive defense mechanism against PAHs, which opens new avenues for the research of phytoremediation mechanism and improvement of phytoremediation efficiency via a mechanism-based strategy.

High-resolution magic angle spinning NMR for intact biological specimen analysis: Initial discovery, recent developments, and future directions

High-resolution magic angle spinning (HRMAS) NMR, an approach for intact biological material analysis discovered more than 25 years ago, has been advanced by many technical developments and applied to many biomedical uses. This article provides a history of its discovery, first by explaining the key scientific advances that paved the way for HRMAS NMR's invention, and then by turning to recent developments that have profited from applying and advancing the technique during the last 5 years. Developments aimed at directly impacting healthcare include HRMAS NMR metabolomics applications within studies of human disease states such as cancers, brain diseases, metabolic diseases, transplantation medicine, and adiposity. Here, the discussion describes recent HRMAS NMR metabolomics studies of breast cancer and prostate cancer, as well as of matching tissues with biofluids, multimodality studies, and mechanistic investigations, all conducted to better understand disease metabolic characteristics for diagnosis, opportune windows for treatment, and prognostication. In addition, HRMAS NMR metabolomics studies of plants, foods, and cell structures, along with longitudinal cell studies, are reviewed and discussed. Finally, inspired by the technique's history of discoveries and recent successes, future biomedical arenas that stand to benefit from HRMAS NMR-initiated scientific investigations are presented.

Spatially specific mechanisms and functions of the plant circadian clock

Like many organisms, plants have evolved a genetic network, the circadian clock, to coordinate processes with day/night cycles. In plants, the clock is a pervasive regulator of development and modulates many aspects of physiology. Clock-regulated processes range from the correct timing of growth and cell division to interactions with the root microbiome. Recently developed techniques, such as single-cell time-lapse microscopy and single-cell RNA-seq, are beginning to revolutionize our understanding of this clock regulation, revealing a surprising degree of organ, tissue, and cell-type specificity. In this review, we highlight recent advances in our spatial view of the clock across the plant, both in terms of how it is regulated and how it regulates a diversity of output processes. We outline how understanding these spatially specific functions will help reveal the range of ways that the clock provides a fitness benefit for the plant.

Untargeted and Targeted Circadian Metabolomics Using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) and Flow Injection-Electrospray Ionization-Tandem Mass Spectrometry (FIA-ESI-MS/MS)

A diverse array of 24-h oscillating hormones and metabolites direct and reflect circadian clock function. Circadian metabolomics uses advanced high-throughput analytical chemistry techniques to comprehensively profile these small molecules (<1.5 kDa) across 24 h in cells, media, body fluids, breath, tissues, and subcellular compartments. The goals of circadian metabolomics experiments are often multifaceted. These include identifying and tracking rhythmic metabolic inputs and outputs of central and peripheral circadian clocks, quantifying endogenous free-running period, monitoring relative phase alignment between clocks, and mapping pathophysiological consequences of clock disruption or misalignment. Depending on the particular experimental question, samples are collected under free-running or entrained conditions. Here we describe both untargeted and targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) and flow injection-electrospray ionization-tandem mass spectrometry (FIA-ESI-MS/MS) based assays we have used for circadian metabolomics studies. We discuss tissue homogenization, chemical derivatization, measurement, and tips for data processing, normalization, scaling, how to handle outliers, and imputation of missing values.

Fine mapping identifies NAD-ME1 as a candidate underlying a major locus controlling temporal variation in primary and specialized metabolism in Arabidopsis

Plant metabolism is modulated by a complex interplay between internal signals and external cues. A major goal of all quantitative metabolomic studies is to clone the underlying genes to understand the mechanistic basis of this variation. Using fine-scale genetic mapping, in this work we report the identification and initial characterization of NAD-DEPENDENT MALIC ENZYME 1 (NAD-ME1) as the candidate gene underlying the pleiotropic network Met.II.15 quantitative trait locus controlling variation in plant metabolism and circadian clock outputs in the Bay × Sha Arabidopsis population. Transcript abundance and promoter analysis in NAD-ME1^Bay-0 and NAD-ME1^Sha alleles confirmed allele-specific expression that appears to be due a polymorphism disrupting a putative circadian cis-element binding site. Analysis of transfer DNA insertion lines and heterogeneous inbred families showed that transcript variation of the NAD-ME1 gene led to temporal shifts of tricarboxylic acid cycle intermediates, glucosinolate (GSL) accumulation, and altered regulation of several GSL biosynthesis pathway genes. Untargeted metabolomic analyses revealed complex regulatory networks of NAD-ME1 dependent upon the daytime. The mutant led to shifts in plant primary metabolites, cell wall components, isoprenoids, fatty acids, and plant immunity phytochemicals, among others. Our findings suggest that NAD-ME1 may act as a key gene to coordinate plant primary and secondary metabolism in a time-dependent manner.

HR-MAS NMR Applications in Plant Metabolomics

Metabolomics is used to reduce the complexity of plants and to understand the underlying pathways of the plant phenotype. The metabolic profile of plants can be obtained by mass spectrometry or liquid-state NMR. The extraction of metabolites from the sample is necessary for both techniques to obtain the metabolic profile. This extraction step can be eliminated by making use of high-resolution magic angle spinning (HR-MAS) NMR. In this review, an HR-MAS NMR-based workflow is described in more detail, including used pulse sequences in metabolomics. The pre-processing steps of one-dimensional HR-MAS NMR spectra are presented, including spectral alignment, baseline correction, bucketing, normalisation and scaling procedures. We also highlight some of the models which can be used to perform multivariate analysis on the HR-MAS NMR spectra. Finally, applications of HR-MAS NMR in plant metabolomics are described and show that HR-MAS NMR is a powerful tool for plant metabolomics studies.

Involvement of BGLU30 in Glucosinolate Catabolism in the Arabidopsis Leaf under Dark Conditions

Glucosinolates (GSLs) are secondary metabolites that play important roles in plant defense and are suggested to act as storage compounds. Despite their important roles, metabolic dynamics of GSLs under various growth conditions remain poorly understood. To determine how light conditions influence the levels of different GSLs and their distribution in Arabidopsis leaves, we visualized the GSLs under different light conditions using matrix-assisted laser desorption/ionization mass spectrometry imaging. We observed the unique distribution patterns of each GSL in the inner regions of leaves and marked decreases under darkness, indicating light conditions influenced GSL metabolism. GSLs are hydrolyzed by a group of ß-glucosidase (BGLU) called myrosinase. Previous transcriptome data for GSL metabolism under light and dark conditions have revealed the highly induced expression of BGLU30, one of the putative myrosinases, which is also annotated as Dark INducible2, under darkness. Impairment of the darkness-induced GSL decrease in the disruption mutants of BGLU30, bglu30, indicated that BGLU30 mediated GSL hydrolysis under darkness. Based on the GSL profiles in the wild-type and bglu30 leaves under both conditions, short-chain GSLs were potentially preferable substrates for BGLU30. Our findings provide an effective way of visualizing GSL distribution in plants and highlighted the carbon storage GSL function.