scholarly journals Retrograde sulfur flow from glucosinolates to cysteine in Arabidopsis thaliana

2021 ◽  
Vol 118 (22) ◽  
pp. e2017890118
Author(s):  
Ryosuke Sugiyama ◽  
Rui Li ◽  
Ayuko Kuwahara ◽  
Ryo Nakabayashi ◽  
Naoyuki Sotta ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
General Interest ◽  
Sulfur Source ◽  
Primary Metabolism ◽  
Plant Metabolites ◽  
Primary Metabolite ◽  
Primary Metabolites ◽  
Specialized Metabolites ◽  
End Products ◽  
Tracer Experiments

Specialized (secondary) metabolic pathways in plants have long been considered one-way routes of leading primary metabolite precursors to bioactive end products. Conversely, endogenous degradation of such “end” products in plant tissues has been observed following environmental stimuli, including nutrition stress. Therefore, it is of general interest whether specialized metabolites can be reintegrated into primary metabolism to recover the invested resources, especially in the case of nitrogen- or sulfur-rich compounds. Here, we demonstrate that endogenous glucosinolates (GLs), a class of sulfur-rich plant metabolites, are exploited as a sulfur source by the reallocation of sulfur atoms to primary metabolites such as cysteine in Arabidopsis thaliana. Tracer experiments using 34S- or deuterium-labeled GLs depicted the catabolic processing of GL breakdown products in which sulfur is mobilized from the thioglucoside group in GL molecules, potentially accompanied by the release of the sulfate group. Moreover, we reveal that beta-glucosidases BGLU28 and BGLU30 are the major myrosinases that initiate sulfur reallocation by hydrolyzing particular GL species, conferring sulfur deficiency tolerance in A. thaliana, especially during early development. The results delineate the physiological function of GL as a sulfur reservoir, in addition to their well-known functions as defense chemicals. Overall, our findings demonstrate the bidirectional interaction between primary and specialized metabolism, which enhances our understanding of the underlying metabolic mechanisms via which plants adapt to their environments.

Metabolic Fingerprinting and Profiling of Arabidopsis thaliana Leaf and its Cultured Cells T87 by GC/MS

2006 ◽  
Vol 61 (3-4) ◽  
pp. 267-272 ◽  
Author(s):  
Eiichiro Fukusaki ◽  
Kanokwan Jumtee ◽  
Takeshi Bamba ◽  
Takehiro Yamaji ◽  
Akio Kobayashi
Keyword(s):  
Arabidopsis Thaliana ◽  
Cell Suspension ◽  
Cultured Cells ◽  
Cell Suspension Cultures ◽  
Metabolite Profile ◽  
Culture Cell ◽  
Suspension Cultures ◽  
Primary Metabolite ◽  
Primary Metabolites ◽  
Suspension Culture Cell

Cell suspension cultures are now recognized as important model materials for plant bioscience and biotechnology. Very few studies of metabolic comparisons between cell cultures and original plants have been reported, even though the biological identity of cultured cells with the normally grown plant is of great importance. In this study, a comparison of the metabolome for primary metabolites extracted from the leaves of Arabidopsis thaliana and cultured cells from an Arabidopsis suspension culture (cell line T87) was performed. The results suggest that although cell suspension cultures and Arabidopsis leaves showed similarities in the common primary metabolite profile, nonetheless, moderate differences in quantitative profile were revealed.

scholarly journals Plant secondary metabolites as defenses, regulators and primary metabolites- The blurred functional trichotomy

2020 ◽  
Author(s):  
Matthias Erb ◽  
Daniel J. Kliebenstein
Keyword(s):  
Secondary Metabolites ◽  
Plant Growth ◽  
Plant Secondary Metabolites ◽  
Trophic Levels ◽  
Primary Metabolism ◽  
Plant Metabolites ◽  
Small Molecular Weight ◽  
Primary Metabolites ◽  
Environmental Selection ◽  
Plant Environment

The plant kingdom produces hundreds of thousands of small molecular weight organic compounds. Based on their assumed functions, the research community has classified them into three overarching groups: primary metabolites which are directly required for plant growth, secondary (or specialized) metabolites which mediate plant-environment interactions and hormones which regulate organismal processes, including metabolism. For decades, this functional trichotomy has shaped theory and experimentation in plant biology. However, evidence is accumulating that the boundaries between the different types of metabolites are blurred. An increasing number of mechanistic studies demonstrate that secondary metabolites are multifunctional and can act as potent regulators of plant growth and defense. Secondary metabolites are also re-integrated into primary metabolism, thus behaving like primary metabolites sensu lato. Several adaptive scenarios may have favored this functional diversity for secondary metabolites, including signaling robustness and cost-effective storage and recycling. Secondary metabolite multi-functionality can provide new explanations for ontogenetic patterns of defense production and can refine our understanding of plant-herbivore interactions, in particular by accounting for the discovery that adapted herbivores misuse plant secondary metabolites for multiple purposes, some of which mirror their functions in plants. In conclusion, recent work unveils the limits of our current classification system for plant metabolites and suggests that viewing them as integrated components of metabolic networks that are dynamically shaped by environmental selection pressures and transcend multiple trophic levels can improve our understanding of plant metabolism and plant-environment interactions.

scholarly journals Evidence that ACN1 (acetate non-utilizing 1) prevents carbon leakage from peroxisomes during lipid mobilization in Arabidopsis seedlings

2011 ◽  
Vol 437 (3) ◽  
pp. 505-513 ◽  
Author(s):  
Elizabeth Allen ◽  
Annick Moing ◽  
Jonathan A. D. Wattis ◽  
Tony Larson ◽  
Mickaël Maucourt ◽  
...  
Keyword(s):  
Carbon Sink ◽  
Glyoxylate Cycle ◽  
Eicosenoic Acid ◽  
Primary Metabolism ◽  
Acetyl Coa ◽  
Primary Metabolite ◽  
Lipid Mobilization ◽  
Transcript Levels ◽  
Chain Acyl ◽  
Acetate Accumulation

ACN1 (acetate non-utilizing 1) is a short-chain acyl-CoA synthetase which recycles free acetate to acetyl-CoA in peroxisomes of Arabidopsis. Pulse-chase [2-13C]acetate feeding of the mutant acn1–2 revealed that acetate accumulation and assimilation were no different to that of wild-type, Col-7. However, the lack of acn1–2 led to a decrease of nearly 50% in 13C-labelling of glutamine, a major carbon sink in seedlings, and large decreases in primary metabolite levels. In contrast, acetyl-CoA levels were higher in acn1–2 compared with Col-7. The disappearance of eicosenoic acid was slightly delayed in acn1–2 indicating only a small effect on the rate of lipid breakdown. A comparison of transcript levels in acn1–2 and Col-7 showed that induced genes included a number of metabolic genes and also a large number of signalling-related genes. Genes repressed in the mutant were represented primarily by embryogenesis-related genes. Transcript levels of glyoxylate cycle genes also were lower in acn1–2 than in Col-7. We conclude that deficiency in peroxisomal acetate assimilation comprises only a small proportion of total acetate use, but this affects both primary metabolism and gene expression. We discuss the possibility that ACN1 safeguards against the loss of carbon as acetate from peroxisomes during lipid mobilization.

The effect of plant metabolites on coronaviruses: A comprehensive review focusing on their IC50 values and molecular docking scores

2021 ◽  
Vol 21 ◽  
Author(s):  
Parastou Farshi ◽  
Eda Ceren Kaya ◽  
Fataneh Hashempour-Baltork ◽  
Kianoush Khosravi-Darani
Keyword(s):  
Molecular Docking ◽  
Inhibitory Effect ◽  
Organosulfur Compounds ◽  
Amino Acid Residues ◽  
Plant Metabolites ◽  
Primary Metabolites ◽  
Secondary Plant Metabolites ◽  
Protein Receptors ◽  
Ic50 Values ◽  
Natural Drugs

: Coronaviruses have caused worldwide outbreaks in different periods. SARS (severe acute respiratory syndrome), was the first emerged virus from this family, followed by MERS (Middle East respiratory syndrome) and SARS-CoV-2 (2019-nCoV or COVID 19), which is newly emerged. Many studies have been conducted on the application of chemical and natural drugs for treating these coronaviruses and they are mostly focused on inhibiting the proteases of viruses or blocking their protein receptors through binding to amino acid residues. Among many substances which are introduced to have an inhibitory effect against coronaviruses through the mentioned pathways, natural components are of specific interest. Secondary and primary metabolites from plants, are considered as potential drugs to have an inhibitory effect on coronaviruses. IC50 value (the concentration in which there is 50% loss in enzyme activity), molecular docking score and binding energy are parameters to understand the ability of metabolites to inhibit the specific virus. In this study we did a review of 154 papers on the effect of plant metabolites on different coronaviruses and data of their IC50 values, molecular docking scores and inhibition percentages are collected in tables. Secondary plant metabolites such as polyphenol, alkaloids, terpenoids, organosulfur compounds, saponins and saikosaponins, lectins, essential oil, and nicotianamine, and primary metabolites such as vitamins are included in this study.

scholarly journals Perturbations in the Primary Metabolism of Tomato and Arabidopsis thaliana Plants Infected with the Soil-Borne Fungus Verticillium dahliae

PLoS ONE ◽  
2015 ◽  
Vol 10 (9) ◽  
pp. e0138242 ◽  
Author(s):  
Anja Buhtz ◽  
Katja Witzel ◽  
Nadine Strehmel ◽  
Jörg Ziegler ◽  
Steffen Abel ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Verticillium Dahliae ◽  
Primary Metabolism

scholarly journals A Metabolic Signature of the Beneficial Interaction of the Endophyte Paenibacillus sp. Isolate and In Vitro–Grown Poplar Plants Revealed by Metabolomics

2009 ◽  
Vol 22 (8) ◽  
pp. 1032-1037 ◽  
Author(s):  
Christian Scherling ◽  
Kristina Ulrich ◽  
Dietrich Ewald ◽  
Wolfram Weckwerth
Keyword(s):  
Endophytic Bacteria ◽  
Tricarboxylic Acid Cycle ◽  
Primary Metabolism ◽  
Plant Metabolites ◽  
Metabolic Signature ◽  
Mutualistic Interaction ◽  
Paenibacillus Sp ◽  
Plant Growth Promoting ◽  
Growth Promoting

Metabolic profiling via gas chromatography coupled to mass spectrometry was used to investigate the influence of endophytic bacteria on shoots of in vitro-grown poplar plants free from culturable endophytic bacteria. The results demonstrate that the occurrence of an endophytic Paenibacillus strain strongly affects the composition of the plant metabolites of in vitro-grown poplars. Eleven metabolites were significantly changed between inoculated and non-inoculated poplar plants as determined by two independent experiments. Detected shifts in the primary metabolism of the poplar plants pointed to a mutualistic interaction between bacteria able to fix nitrogen and the host plant with altered nitrogen assimilation patterns. The corresponding metabolic signature comprises increased asparagine and urea levels as well as depleted sugars and organic acids of the tricarboxylic acid cycle. These observations coincide with the fact that the Paenibacillus sp. strain P22 is able to grow without nitrogen in the medium, indicating nitrogen fixation from the air also known from other Paenibacillus spp. In combination with the detected plant-growth-promoting effects of the endophyte Paenibacillus P22, a novel mutualistic interaction is observed.

Arginine metabolism of Arabidopsis thaliana is modulated by Heterodera schachtii infection

Nematology ◽  
2015 ◽  
Vol 17 (9) ◽  
pp. 1027-1043 ◽  
Author(s):  
Shahbaz Anwar ◽  
Erich Inselsbacher ◽  
Florian M.W. Grundler ◽  
Julia Hofmann
Keyword(s):  
Arabidopsis Thaliana ◽  
Amino Acid ◽  
Stress Responses ◽  
Plant Stress ◽  
Heterodera Schachtii ◽  
Primary Metabolism ◽  
Arginine Metabolism ◽  
Significant Difference ◽  
Amino Acid Levels ◽  
Nematode Development

The plant-parasitic cyst nematode Heterodera schachtii induces syncytial feeding structures in the roots of host plants. These syncytia provide all required nutrients, water and solutes to the parasites. Previous studies on the composition of primary metabolites in syncytia revealed significantly increased amino acid levels. However, mainly due to technical limitations, little is known about the role of arginine in plant-nematode interactions. This free amino acid plays a central role in the plant primary metabolism and serves as substrate for metabolites involved in plant stress responses. Thus, in the present work, expression of genes coding for the enzymes of arginine metabolism were studied in nematode-induced syncytia compared to non-infected control roots of Arabidopsis thaliana. Further, amiRNA lines were constructed and T-DNA lines were isolated to test their effects on nematode development. While the silencing of genes involved in arginine synthesis increased nematode development, most T-DNA lines did not show any significant difference from the wild type. Amino acid analyses of syncytia showed that they accumulate high arginine levels. In addition, manipulating arginine cycling had a global effect on the local amino acid composition in syncytia as well as on the systemic amino acid levels in roots and shoots.

scholarly journals Multiplex Genome Editing in Yeast by CRISPR/Cas9 – A Potent and Agile Tool to Reconstruct Complex Metabolic Pathways

2021 ◽  
Vol 12 ◽  
Author(s):  
Joseph Christian Utomo ◽  
Connor Lorne Hodgins ◽  
Dae-Kyun Ro
Keyword(s):  
Genome Editing ◽  
Metabolic Pathways ◽  
Functional Characterization ◽  
Primary Metabolism ◽  
Biosynthetic Pathways ◽  
Post Translational Modification ◽  
Precise Integration ◽  
Specialized Metabolism ◽  
Specialized Metabolites ◽  
Plant Specialized Metabolism

Numerous important pharmaceuticals and nutraceuticals originate from plant specialized metabolites, most of which are synthesized via complex biosynthetic pathways. The elucidation of these pathways is critical for the applicable uses of these compounds. Although the rapid progress of the omics technology has revolutionized the identification of candidate genes involved in these pathways, the functional characterization of these genes remains a major bottleneck. Baker’s yeast (Saccharomyces cerevisiae) has been used as a microbial platform for characterizing newly discovered metabolic genes in plant specialized metabolism. Using yeast for the investigation of numerous plant enzymes is a streamlined process because of yeast’s efficient transformation, limited endogenous specialized metabolism, partially sharing its primary metabolism with plants, and its capability of post-translational modification. Despite these advantages, reconstructing complex plant biosynthetic pathways in yeast can be time intensive. Since its discovery, CRISPR/Cas9 has greatly stimulated metabolic engineering in yeast. Yeast is a popular system for genome editing due to its efficient homology-directed repair mechanism, which allows precise integration of heterologous genes into its genome. One practical use of CRISPR/Cas9 in yeast is multiplex genome editing aimed at reconstructing complex metabolic pathways. This system has the capability of integrating multiple genes of interest in a single transformation, simplifying the reconstruction of complex pathways. As plant specialized metabolites usually have complex multigene biosynthetic pathways, the multiplex CRISPR/Cas9 system in yeast is suited well for functional genomics research in plant specialized metabolism. Here, we review the most advanced methods to achieve efficient multiplex CRISPR/Cas9 editing in yeast. We will also discuss how this powerful tool has been applied to benefit the study of plant specialized metabolism.

scholarly journals Robust predictions of specialized metabolism genes through machine learning

2018 ◽  
Author(s):  
Bethany M. Moore ◽  
Peipei Wang ◽  
Pengxiang Fan ◽  
Bryan Leong ◽  
Craig A. Schenck ◽  
...  
Keyword(s):  
Machine Learning ◽  
Prediction Model ◽  
Gene Networks ◽  
Experimental Studies ◽  
Plant Genome ◽  
Primary Metabolism ◽  
Specialized Metabolism ◽  
Specialized Metabolites ◽  
General Metabolism ◽  
Pattern Sequence

AbstractPlant specialized metabolism (SM) enzymes produce lineage-specific metabolites with important ecological, evolutionary, and biotechnological implications. Using Arabidopsis thaliana as a model, we identified distinguishing characteristics of SM and GM (general metabolism, traditionally referred to as primary metabolism) genes through a detailed study of features including duplication pattern, sequence conservation, transcription, protein domain content, and gene network properties. Analysis of multiple sets of benchmark genes revealed that SM genes tend to be tandemly duplicated, co-expressed with their paralogs, narrowly expressed at lower levels, less conserved, and less well connected in gene networks relative to GM genes. Although the values of each of these features significantly differed between SM and GM genes, any single feature was ineffective at predicting SM from GM genes. Using machine learning methods to integrate all features, a well performing prediction model was established with a true positive rate of 0.87 and a true negative rate of 0.71. In addition, 86% of known SM genes not used to create the machine learning model were predicted as SM genes, further demonstrating its accuracy. We also demonstrated that the model could be further improved when we distinguished between SM, GM, and junction genes responsible for reactions shared by SM and GM pathways. Application of the prediction model led to the identification of 1,217 A. thaliana genes with previously unknown functions, providing a global, high-confidence estimate of SM gene content in a plant genome.SignificanceSpecialized metabolites are critical for plant-environment interactions, e.g., attracting pollinators or defending against herbivores, and are important sources of plant-based pharmaceuticals. However, it is unclear what proportion of enzyme-encoding genes play roles in specialized metabolism (SM) as opposed to general metabolism (GM) in any plant species. This is because of the diversity of specialized metabolites and the considerable number of incompletely characterized pathways responsible for their production. In addition, SM gene ancestors frequently played roles in GM. We evaluate features distinguishing SM and GM genes and build a computational model that accurately predicts SM genes. Our predictions provide candidates for experimental studies, and our modeling approach can be applied to other species that produce medicinally or industrially useful compounds.

Sign in / Sign up

Export Citation Format

Share Document