skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


This content will become publicly available on January 1, 2026

Title: AraRoot—a comprehensive genome-scale metabolic model for the Arabidopsis root system
Abstract Being the first plant to have its genome sequenced, Arabidopsis thaliana (Arabidopsis) is a well-established genetic model plant system. Studies on Arabidopsis have provided major insights into the physiological and biochemical nature of plants. Methods that allow us to study organisms’ metabolism computationally include using genome-scale metabolic models (GEMs). Despite its popularity, no GEM currently maps the metabolic activity in the roots of Arabidopsis, which is the organ that faces and responds to stress conditions in the soil. We have developed a comprehensive metabolic model of the Arabidopsis root system—AraRoot. The final model includes 2,682 reactions, 2,748 metabolites, and 1,310 genes. Analyzing the metabolic pathways in this model identified 158 possible bottleneck genes that impact biomass production, most of which were found to be related to phosphorous-containing- and energy-related pathways. Further insights into tissue-specific metabolic reprogramming conclude that the cortex layer in the roots is likely responsible for root growth under prolonged exposure to high salt conditions. At the same time, the endodermis and epidermis are responsible for producing metabolites responsible for increased cell wall biosynthesis. The epidermis was found to have a very poor ability to regulate its metabolism during exposure to high salt concentrations. Overall, AraRoot is the first metabolic model that comprehensively captures the biomass formation and stress responses of the tissues in the Arabidopsis root system.  more » « less
Award ID(s):
2212800 2212799 2212801
PAR ID:
10608166
Author(s) / Creator(s):
; ; ; ; ;
Editor(s):
Marshall-Colon, Amy
Publisher / Repository:
Oxford University Press
Date Published:
Journal Name:
in silico Plants
Volume:
7
Issue:
1
ISSN:
2517-5025
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; ; ; (, Journal of Experimental Botany)
    Gibon, Yves (Ed.)
    Abstract The growth and development of maize (Zea mays L.) largely depends on its nutrient uptake through the root. Hence, studying its growth, response, and associated metabolic reprogramming to stress conditions is becoming an important research direction. A genome-scale metabolic model (GSM) for the maize root was developed to study its metabolic reprogramming under nitrogen stress conditions. The model was reconstructed based on the available information from KEGG, UniProt, and MaizeCyc. Transcriptomics data derived from the roots of hydroponically grown maize plants were used to incorporate regulatory constraints in the model and simulate nitrogen-non-limiting (N+) and nitrogen-deficient (N−) condition. Model-predicted flux-sum variability analysis achieved 70% accuracy compared with the experimental change of metabolite levels. In addition to predicting important metabolic reprogramming in central carbon, fatty acid, amino acid, and other secondary metabolism, maize root GSM predicted several metabolites (l-methionine, l-asparagine, l-lysine, cholesterol, and l-pipecolate) playing a regulatory role in the root biomass growth. Furthermore, this study revealed eight phosphatidylcholine and phosphatidylglycerol metabolites which, even though not coupled with biomass production, played a key role in the increased biomass production under N-deficient conditions. Overall, the omics-integrated GSM provides a promising tool to facilitate stress condition analysis for maize root and engineer better stress-tolerant maize genotypes. 
    more » « less
  2. ; ; ; ; (, BMC Plant Biology)
    Abstract Background Plant growth promoting rhizobacteria (PGPR) , such as Bradyrhizobium japonicum IRAT FA3, are able to improve seed germination and plant growth under various biotic and abiotic stress conditions, including high salinity stress. PGPR can affect plants’ responses to stress via multiple pathways which are often interconnected but were previously thought to be distinct. Although the overall impacts of PGPR on plant growth and stress tolerance have been well documented, the underlying mechanisms are not fully elucidated. This work contributes to understanding how PGPR promote abiotic stress by revealing major plant pathways triggered by B. japonicum under salt stress. Results The plant growth-promoting rhizobacterial (PGPR) strain Bradyrhizobium japonicum IRAT FA3 reduced the levels of sodium in Arabidopsis thaliana by 37.7% . B. japonicum primed plants as it stimulated an increase in jasmonates (JA) and modulated hydrogen peroxide production shortly after inoculation. B. japonicum -primed plants displayed enhanced shoot biomass, reduced lipid peroxidation and limited sodium accumulation under salt stress conditions. Q(RT)-PCR analysis of JA and abiotic stress-related gene expression in Arabidopsis plants pretreated with B. japonicum and followed by six hours of salt stress revealed differential gene expression compared to non-inoculated plants. Response to Desiccation ( RD ) gene RD20 and reactive oxygen species scavenging genes CAT3 and MDAR2 were up-regulated in shoots while CAT3 and RD22 were increased in roots by B. japonicum , suggesting roles for these genes in B. japonicum -mediated salt tolerance. B. japonicum also influenced reductions of RD22 , MSD1 , DHAR and MYC2 in shoots and DHAR , ADC2 , RD20 , RD29B , GTR1 , ANAC055 , VSP1 and VSP2 gene expression in roots under salt stress. Conclusion Our data showed that MYC2 and JAR1 are required for B. japonicum -induced shoot growth in both salt stressed and non-stressed plants. The observed microbially influenced reactions to salinity stress in inoculated plants underscore the complexity of the B. japonicum jasmonic acid-mediated plant response salt tolerance. 
    more » « less
  3. ; ; ; ; ; ; ; ; ; ; et al (, Chemical Research in Toxicology)
    null (Ed.)
    Growing evidence across organisms points to altered energy metabolism as an adverse outcome of metal oxide nanomaterial toxicity, with a mechanism of toxicity potentially related to the redox chemistry of processes involved in energy production. Despite this evidence, the significance of this mechanism has gone unrecognized in nanotoxicology due to the field’s focus on oxidative stress as a universal—but non-specific—nanotoxicity mechanism. To further explore metabolic impacts, we determined LCO’s effects on these pathways in the model organism Daphnia magna through global gene expression analysis using RNA-Seq and untargeted metabolomics by direct-injection mass spectrometry. Our results show a sublethal 1 mg/L 48 h exposure of D. magna to LCO nanosheets causes significant impacts on metabolic pathways versus untreated controls, while exposure to ions released over 48 hr does not. Specifically, transcriptomic analysis using DAVID indicated significant enrichment (Benjamini-adjusted p ≤0.0.5) in LCO-exposed animals for changes in pathways involved in the cellular response to starvation (25 genes), mitochondrial function (70 genes), ATP-binding (70 genes), oxidative phosphorylation (53 genes), NADH dehydrogenase activity (12 genes), and protein biosynthesis (40 genes). Metabolomic analysis using MetaboAnalyst indicated significant enrichment (gamma-adjusted p < 0.1) for changes in amino acid metabolism (19 metabolites) and starch, sucrose, and galactose metabolism (7 metabolites). Overlap of significantly impacted pathways by RNA-Seq and metabolomics suggests amino acid breakdown and increased sugar import for energy production. Results indicate that LCO-exposed Daphnia are responding to energy starvation by altering metabolic pathways, both at the gene expression and metabolite level. These results support altered energy production as a sensitive nanotoxicity adverse outcome for LCO exposure and suggest negative impacts on energy metabolism as an important avenue for future studies of nanotoxicity, including for other biological systems and for metal oxide nanomaterials more broadly. 
    more » « less
  4. ; ; ; ; ; ; (, Science Advances)
    Tremendous plant metabolic diversity arises from phylogenetically restricted specialized metabolic pathways. Specialized metabolites are synthesized in dedicated cells or tissues, with pathway genes sometimes colocalizing in biosynthetic gene clusters (BGCs). However, the mechanisms by which spatial expression patterns arise and the role of BGCs in pathway evolution remain underappreciated. In this study, we investigated the mechanisms driving acylsugar evolution in the Solanaceae. Previously thought to be restricted to glandular trichomes, acylsugars were recently found in cultivated tomato roots. We demonstrated that acylsugars in cultivated tomato roots and trichomes have different sugar cores, identified root-enriched paralogs of trichome acylsugar pathway genes, and characterized a key paralog required for root acylsugar biosynthesis,SlASAT1-LIKE(SlASAT1-L), which is nested within a previously reported trichome acylsugar BGC. Last, we provided evidence thatASAT1-Larose through duplication of its paralog,ASAT1, and was trichome-expressed before acquiring root-specific expression in theSolanumgenus. Our results illuminate the genomic context and molecular mechanisms underpinning metabolic diversity in plants. 
    more » « less
  5. ; ; ; ; ; ; ; ; ; ; et al (, eLife)
    Soil salinity is one of the major threats to agricultural productivity worldwide. Salt stress exposure alters root and shoots growth rates, thereby affecting overall plant performance. While past studies have extensively documented the effect of salt stress on root elongation and shoot development separately, here we take an innovative approach by examining the coordination of root and shoot growth under salt stress conditions. Utilizing a newly developed tool for quantifying the root:shoot ratio in agar-grownArabidopsisseedlings, we found that salt stress results in a loss of coordination between root and shoot growth rates. We identify a specific gene cluster encoding domain-of-unknown-function 247 (DUF247), and characterize one of these genes asSaltRoot:shootRatioRegulatorGene (SR3G). Further analysis elucidates the role of SR3G as a negative regulator of salt stress tolerance, revealing its function in regulating shoot growth, root suberization, and sodium accumulation. We further characterize thatSR3Gexpression is modulated byWRKY75transcription factor, known as a positive regulator of salt stress tolerance. Finally, we show that the salt stress sensitivity ofwrky75mutant is completely diminished when it is combined withsr3gmutation. Together, our results demonstrate that utilizing root:shoot ratio as an architectural feature leads to the discovery of a new stress resilience gene. The study’s innovative approach and findings not only contribute to our understanding of plant stress tolerance mechanisms but also open new avenues for genetic and agronomic strategies to enhance crop environmental resilience. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email