Fruit set is the process whereby ovaries develop into fruits after pollination and fertilization. The process is induced by the phytohormone gibberellin (GA) in tomatoes, as determined by the ...constitutive GA response mutant procera. However, the role of GA on the metabolic behavior in fruit-setting ovaries remains largely unknown. This study explored the biochemical mechanisms of fruit set using a network analysis of integrated transcriptome, proteome, metabolome, and enzyme activity data. Our results revealed that fruit set involves the activation of central carbon metabolism, with increased hexoses, hexose phosphates, and downstream metabolites, including intermediates and derivatives of glycolysis, the tricarboxylic acid cycle, and associated organic and amino acids. The network analysis also identified the transcriptional hub gene SlHB15A, that coordinated metabolic activation. Furthermore, a kinetic model of sucrose metabolism predicted that the sucrose cycle had high activity levels in unpollinated ovaries, whereas it was shut down when sugars rapidly accumulated in vacuoles in fruit-setting ovaries, in a time-dependent manner via tonoplastic sugar carriers. Moreover, fruit set at least partly required the activity of fructokinase, which may pull fructose out of the vacuole, and this could feed the downstream pathways. Collectively, our results indicate that GA cascades enhance sink capacities, by up-regulating central metabolic enzyme capacities at both transcriptional and posttranscriptional levels. This leads to increased sucrose uptake and carbon fluxes for the production of the constituents of biomass and energy that are essential for rapid ovary growth during the initiation of fruit set.
Heterosis contributes greatly to the worldwide agricultural yield. However, the molecular mechanism underlying heterosis remains unclear. This study took advantage of Arabidopsis intraspecific ...hybrids to identify heterosis-related metabolites. Forty-six intraspecific hybrids were used to examine parental effects on seed area and germination time. The degree of heterosis was evaluated based on biomass: combinations showing high heterosis of F
hybrids exhibited a biomass increase from 6.1 to 44% over the better parent value (BPV), whereas that of the low- and no-heterosis hybrids ranged from - 19.8 to 9.8% over the BPV. Metabolomics analyses of F
hybrids with high heterosis and those with low one suggested that changes in TCA cycle intermediates are key factors that control growth. Notably, higher fumarate/malate ratios were observed in the high heterosis F
hybrids, suggesting they provide metabolic support associated with the increased biomass. These hybrids may produce more energy-intensive biomass by speeding up the efficiency of TCA fluxes. However, the expression levels of TCA-process-related genes in F
hybrids were not associated with the intensity of heterosis, suggesting that the post-transcriptional or post-translational regulation of these genes may affect the productivity of the intermediates in the TCA cycle.
Key message
Ethanol priming induces heat stress tolerance by the stimulation of unfolded protein response.
Global warming increases the risk of heat stress-related yield losses in agricultural crops. ...Chemical priming, using safe agents, that can flexibly activate adaptive regulatory responses to adverse conditions, is a complementary approach to genetic improvement for stress adaptation. In the present study, we demonstrated that pretreatment of
Arabidopsis
with a low concentration of ethanol enhances heat tolerance without suppressing plant growth. We also demonstrated that ethanol pretreatment improved leaf growth in lettuce (
Lactuca sativa
L.) plants grown in the field conditions under high temperatures. Transcriptome analysis revealed a set of genes that were up-regulated in ethanol-pretreated plants, relative to water-pretreated controls.
Binding Protein 3 (BIP3),
an endoplasmic reticulum (ER)-stress marker chaperone gene, was among the identified up-regulated genes. The expression levels of
BIP3
were confirmed by RT-qPCR. Root-uptake of ethanol was metabolized to organic acids, nucleic acids, amines and other molecules, followed by an increase in putrescine content, which substantially promoted unfolded protein response (UPR) signaling and high-temperature acclimation. We also showed that inhibition of polyamine production and UPR signaling negated the heat stress tolerance induced by ethanol pretreatment. These findings collectively indicate that ethanol priming activates UPR signaling via putrescine accumulation, leading to enhanced heat stress tolerance. The information gained from this study will be useful for establishing ethanol-mediated chemical priming strategies that can be used to help maintain crop production under heat stress conditions.
Development of RIKEN Plant Metabolome MetaDatabase Fukushima, Atsushi; Takahashi, Mikiko; Nagasaki, Hideki ...
Plant & cell physiology/Plant and cell physiology,
03/2022, Letnik:
63, Številka:
3
Journal Article
Recenzirano
Odprti dostop
Abstract
The advancement of metabolomics in terms of techniques for measuring small molecules has enabled the rapid detection and quantification of numerous cellular metabolites. Metabolomic data ...provide new opportunities to gain a deeper understanding of plant metabolism that can improve the health of both plants and humans that consume them. Although major public repositories for general metabolomic data have been established, the community still has shortcomings related to data sharing, especially in terms of data reanalysis, reusability and reproducibility. To address these issues, we developed the RIKEN Plant Metabolome MetaDatabase (RIKEN PMM, http://metabobank.riken.jp/pmm/db/plantMetabolomics), which stores mass spectrometry-based (e.g. gas chromatography–MS-based) metabolite profiling data of plants together with their detailed, structured experimental metadata, including sampling and experimental procedures. Our metadata are described as Linked Open Data based on the Resource Description Framework using standardized and controlled vocabularies, such as the Metabolomics Standards Initiative Ontology, which are to be integrated with various life and biomedical science data using the World Wide Web. RIKEN PMM implements intuitive and interactive operations for plant metabolome data, including raw data (netCDF format), mass spectra (NIST MSP format) and metabolite annotations. The feature is suitable not only for biologists who are interested in metabolomic phenotypes, but also for researchers who would like to investigate life science in general through plant metabolomic approaches.
The technological advances in the instrumentation employed in life sciences have enabled the collection of a virtually unlimited quantity of data from multiple sources. By gathering data from several ...analytical platforms, with the aim of parallel monitoring of, e.g. transcriptomic, metabolomic or proteomic events, one hopes to answer and understand biological questions and observations. This 'systems biology' approach typically involves advanced statistics to facilitate the interpretation of the data. In the present study, we demonstrate that the O2PLS multivariate regression method can be used for combining 'omics' types of data. With this methodology, systematic variation that overlaps across analytical platforms can be separated from platform-specific systematic variation. A study of Populus tremula x Populus tremuloides, investigating short-day-induced effects at transcript and metabolite levels, is employed to demonstrate the benefits of the methodology. We show how the models can be validated and interpreted to identify biologically relevant events, and discuss the results in relation to a pairwise univariate correlation approach and principal component analysis.
Arabidopsis PSEUDO RESPONSE REGULATOR (PRR) genes are components of the circadian clock mechanism. In order to understand the scope of genome-wide transcriptional regulation by PRR genes, a ...comparison survey of gene expression in wild-type Arabidopsis and a prr9-11 prr7-10 prr5-10 triple mutant (d975) using mRNA collected during late daytime was conducted using an Affymetrix ATH-1 GeneChipsup(R). The expression of 'night genes' increased and the expression of 'day genes' decreased toward the end of the diurnal tight phase, but expression of these genes was essentially constant in d975. The expression levels of 'night genes' were lower, whereas the expression of 'day genes' was higher in d975 than in the wild type. Bioinformatics approaches have indicated that the set of up-regulated genes in d975 and the set of cold-responsive genes have significant overlap. We found that d975 is more tolerant to cold, high salinity and drought stresses than the wild type. In addition, dehydration-responsive element B1/C-repeat-binding factor (DREB1/CBF), which is expressed around mid-day, is more highly expressed in d975. Raffinose and L-proline accumulated at higher levels in d975 even when plants were grown under normal conditions. These results suggest that PRR9, PRR7 and PRR5 are involved in a mechanism that anticipates diurnal cold stress and which initiates a stress response by mediating cyclic expression of stress response genes, including DREB1/CBF.
Nitrogen (N) is an essential macronutrient, and the final form of endogenous inorganic N is ammonium, which is assimilated by Gln synthetase (GS) into Gln. However, how the multiple isoforms of ...cytosolic GSs contribute to metabolic systems via the regulation of ammonium assimilation remains unclear. In this study, we compared the effects of two rice (
) cytosolic GSs, namely OsGS1;1 and OsGS1;2, on central metabolism in roots using reverse genetics, metabolomic and transcriptomic profiling, and network analyses. We observed (1) abnormal sugar and organic N accumulation and (2) significant up-regulation of genes associated with photosynthesis and chlorophyll biosynthesis in the roots of
but not
knockout mutants. Network analysis of the
mutant suggested that metabolism of Gln was coordinated with the metabolic modules of sugar metabolism, tricarboxylic acid cycle, and carbon fixation. Transcript profiling of
mutant roots revealed that expression of the rice
(
) genes in the mutants were transiently upregulated. GOLDEN2-LIKE transcription factor-encoding genes, which are involved in chloroplast biogenesis in rice, could not compensate for the lack of
s in the
mutant. Microscopic analysis revealed mature chloroplast development in
roots but not in the roots of
,
-complemented lines, or the wild type. Thus, organic N assimilated by OsGS1;1 affects a broad range of metabolites and transcripts involved in maintaining metabolic homeostasis and plastid development in rice roots, whereas OsGS1;2 has a more specific role, affecting mainly amino acid homeostasis but not carbon metabolism.
Fruits of wild tomato species show different ethylene-dependent ripening characteristics, such as variations in fruit color and whether they exhibit a climacteric or nonclimacteric ripening ...transition. 1-Aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS) and ACC oxidase (ACO) are key enzymes in the ethylene biosynthetic pathway encoded by multigene families. Gene duplication is a primary driver of plant diversification and angiosperm evolution. Here, interspecific variations in the molecular regulation of ethylene biosynthesis and perception during fruit ripening in domesticated and wild tomatoes were investigated. Results showed that the activated ACS genes were increased in number in red-ripe tomato fruits than in green-ripe tomato fruits; therefore, elevated dosage of ACS enzyme promoted ripening ethylene production. Results showed that the expression of three ACS isogenes ACS1A, ACS2, and ACS4, which are involved in autocatalytic ethylene production, was higher in red-ripe tomato fruits than in green-ripe tomato fruits. Elevated ACS enzyme dosage promoted ethylene production, which corresponded to the climacteric response of red-ripe tomato fruits. The data suggest that autoinhibitory ethylene production is common to all tomato species, while autocatalytic ethylene production is specific to red-ripe species. The essential regulators Non-ripening (NOR) and Ripening-Inhibitor (RIN) have experienced gene activation and overlapped with increasing ACS enzyme dosage. These complex levels of transcript regulation link higher ethylene production with spatiotemporal modulation of gene expression in red-ripe tomato species. Taken together, this study shows that bursts in ethylene production that accompany fruit color changes in red-ripe tomatoes are likely to be an evolutionary adaptation for seed dispersal.
Display omitted
•The health benefits of Kaempferia spp. include antibacterial, anticancer, antidiabetic, cardiovascular protective, immunoregulatory, neuroprotective, and skin-whitening ...effects.•Bioactive polymethoxyflavones and ethyl p-methoxycinnamate play a role in biological activity of Kaempferia spp..•Kaempferia spp. can target and regulate multiple pathways related to the enhancement of health and vitality.•Studies related to value-added production of K. parviflora, such genotype × environment × management practices are limited.
Kaempferia spp. have traditionally played a role in treating various ailments and are attracting increasing economic and scientific interest. This review evaluates the traditional use, phytochemical compounds, and biological properties of Kaempferia parviflora, Kaempferia galanga, Kaempferia rotunda, Kaempferia pulchra, and Kaempferia angustifolia. The health benefits associated with consuming Kaempferia spp. and their active components, namely flavonoids and other volatile compounds, include antibacterial, anticancer, antidiabetic, cardiovascular protective, immunoregulatory, neuroprotective, and skin-whitening effects, suggesting the use of Kaempferia spp. as a potential health aid for the aging population. As agricultural production is important to ensure consistent quality of Kaempferia produce, resource management techniques related to species identification, cultivation, storage, and processing were also highlighted. It was suggested that the value-added concept in agricultural production may be limited. Investigations into plant biology and physiology are required to provide a solid theoretical basis for the sustainable production of Kaempferia.
Most mass spectrometry based metabolomics studies are semiquantitative and depend on efficient normalization techniques to suppress systematic error. A common approach is to include isotope-labeled ...internal standards (ISs) and then express the estimated metabolite abundances relative to the IS. Because of problems such as insufficient chromatographic resolution, however, the analytes may directly influence estimates of the IS, a phenomenon known as cross-contribution (CC). Normalization using ISs that suffer from CC effects will cause significant loss of information if the interfering analytes are associated with the studied factors. We present a novel normalization algorithm, which compensates for systematic CC effects that can be traced back to a linear association with the experimental design. The proposed method was found to be superior at purifying the signal of interest compared to current normalization methods when applied to two biological data sets and a multicomponent dilution mixture. Our method is applicable to data from randomized and designed experiments that use ISs to monitor the systematic error.
PDF
