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Larbat2016.1 - Modeling the diversion of primary carbon flux into secondary metabolism under variable nitrate and light or dark conditions (Base Model)

ABSTRACT: This is a global mathematical model describing metabolic partitioning of carbon resources in plants between growth and defense, as a function of nitrate fertilization. The model hinges on the dynamics of sucrose inflow/outflow properties.

SUBMITTER: Johannes Meyer

PROVIDER: BIOMD0000000857 | BioModels | 2024-09-02

REPOSITORIES: BioModels

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	BIOMD0000000857?filename=Larbat2016.1-biopax2.owl	Owl
	BIOMD0000000857?filename=Larbat2016.1-biopax3.owl	Owl
	BIOMD0000000857?filename=Larbat2016.1-matlab.m	Other
	BIOMD0000000857?filename=Larbat2016.1-octave.m	Other
	BIOMD0000000857?filename=Larbat2016.1.cps	Other

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Publications

Modeling the diversion of primary carbon flux into secondary metabolism under variable nitrate and light/dark conditions.

Larbat Romain R Robin Christophe C Lillo Cathrine C Drengstig Tormod T Ruoff Peter P

Journal of theoretical biology 20160506

In plants, the partitioning of carbon resources between growth and defense is detrimental for their development. From a metabolic viewpoint, growth is mainly related to primary metabolism including protein, amino acid and lipid synthesis, whereas defense is based notably on the biosynthesis of a myriad of secondary metabolites. Environmental factors, such as nitrate fertilization, impact the partitioning of carbon resources between growth and defense. Indeed, experimental data showed that a shor ...[more]

PMID: 27164436

Similar Datasets

Larbat2016.2 - Modeling the diversion of primary carbon flux into secondary metabolism under variable nitrate and light or dark conditions (Light Dark Cycles)

Project description:This is a global mathematical model describing metabolic partitioning of carbon resources in plants between growth and defense, as a function of nitrate fertilization. The model hinges on the dynamics of sucrose inflow/outflow properties. The model also accounts for variations in photosynthetic activity as dictated by a daily light/dark cycle.

2024-09-02 | BIOMD0000000858 | BioModels

Larbat2016.3 - Modeling the diversion of primary carbon flux into secondary metabolism under variable nitrate and light or dark conditions (Light Dark Cycles with Minimum Starch Adaption)

2024-09-02 | BIOMD0000000859 | BioModels

Proteome Dynamics of Persulfidation in Leaf Tissue under Light/Dark Conditions and Carbon Deprivation.

Project description:Hydrogen sulfide (H2S) acts as a signaling molecule in plants, bacteria, and mammals, regulating various physiological and pathological processes. The molecular mechanism by which hydrogen sulfide exerts its action involves the posttranslational modification of cysteine residues to form a persulfidated thiol motif. This research aimed to study the regulation of protein persulfidation. We used a label-free quantitative approach to measure the protein persulfidation profile in leaves under different growth conditions such as light regimen and carbon deprivation. The proteomic analysis identified a total of 4599 differentially persulfidated proteins, of which 1115 were differentially persulfidated between light and dark conditions. The 544 proteins that were more persulfidated in the dark were analyzed, and showed significant enrichment in functions and pathways related to protein folding and processing in the endoplasmic reticulum. Under light conditions, the persulfidation profile changed, and the number of differentially persulfidated proteins increased up to 913, with the proteasome and ubiquitin-dependent and ubiquitin-independent catabolic processes being the most-affected biological processes. Under carbon starvation conditions, a cluster of 1405 proteins was affected by a reduction in their persulfidation, being involved in metabolic processes that provide primary metabolites to essential energy pathways and including enzymes involved in sulfur assimilation and sulfide production.

| S-EPMC10135009 | biostudies-literature

Exploring Rhodospirillum rubrum response to high doses of carbon monoxide under light and dark conditions.

Project description:Environmental concerns about residues and the traditional disposal methods are driving the search for more environmentally conscious processes, such as pyrolysis and gasification. Their main final product is synthesis gas (syngas) composed of CO, CO2, H2, and methane. Syngas can be converted into various products using CO-tolerant microorganisms. Among them, Rhodospirillum rubrum is highlighted for its biotechnological potential. However, the extent to which high doses of CO affect its physiology is still opaque. For this reason, we have studied R. rubrum behavior under high levels of this gas (up to 2.5 bar), revealing a profound dependence on the presence or absence of light. In darkness, the key variable affected was the lag phase, where the highest levels of CO retarded growth to more than 20 days. Under light, R. rubrum ability to convert CO into CO2 and H2 depended on the presence of an additional carbon source, such as acetate. In those conditions where CO was completely exhausted, CO2 fixation was unblocked, leading to a diauxic growth. To enhance R. rubrum tolerance to CO in darkness, a UV-accelerated adaptive laboratory evolution (UVa-ALE) trial was conducted to isolate clones with shorter lag phases, resulting in the isolation of clones 1.4-2B and 1.7-2A. The adaptation of 1.4-2B was mainly based on mutated enzymes with a metabolic function, while 1.7-3A was mostly affected at regulatory genes, including the anti-repressor PpaA/AerR. Despite these mutations having slight effects on biomass and pigment levels, they successfully provoked a significant reduction in the lag phase (-50%). KEYPOINTS: • CO affects principally R. rubrum lag phase (darkness) and growth rate (light) • CO is converted to CO2/H2 during acetate uptake and inhibits CO2 fixation (light) • UVa-ALE clones showed a 50% reduction in the lag phase (darkness).

| S-EPMC10927898 | biostudies-literature

Transcription profiling of light and carbon signaling interactions in Arabidopsis

Project description:A. thaliana seeds of Columbia (Col-0) ecotype were surface-sterilized, plated on designated media and vernalized for 48 hours at 8C. Plants were grown semi-hydroponically under 16-hr-light, 8-hr-dark cycles at a constant temperature of 23C on basal Murashige and Skoog medium supplemented with 2 mM KNO3, 2 mM NH4NO3 and 30 mM sucrose. Two-week-old seedlings were transferred to fresh MS media without nitrogen and sucrose and dark-adapted for 48 hours. To perform specific metabolic treatments manipulating availability of source of carbon (C) and illumination (L): -C-L, +C-L, -C+L, +C+L, two-week-old seedlings were transferred to fresh MS medium containing 0% or 1% sucrose and either placed back into the dark or illuminated with white light for an additional 8 hours. The various treatments were compared to one another using the treatment of -C-L as the background treatment to which all other treatments (-C+L, +C-L, +C+L) were compared.

2004-01-23 | E-MEXP-71 | biostudies-arrayexpress

Mus musculus

Project description:Transcriptome partitioning in mouse fertilization.

| PRJNA136999 | ENA

Cold acclimation process under limited light conditions in Arabidopsis thaliana

Project description:Plants in temperate regions have evolved mechanisms to survive sudden temperature drops. Previous reports have indicated that the cold acclimation mechanism is light-dependent and does not fully operate under a low light intensity. In these studies, plants were grown under a long-day photoperiod and were more sensitive to freezing stress. However, winter annuals like Arabidopsis thaliana Col-0 germinate in the fall, overwinter as rosettes, and therefore must acclimate under short photoperiods and low irradiance. The role of light intensity was analysed in plants grown under a short-day photoperiod at the growth stage 1.14. Plants were acclimated at 4 °C for seven days under 100 and 20 μmol m-2s-1 PPFD for control and limited-light conditions, respectively. All cold acclimated plants accumulated molecular markers reportedly associated with acquired freezing tolerance, including proline, sucrose, CBFs, and COR gene protein products dehydrins and low-temperature-responsive proteins LTIs. Observed changes indicated that low PPFD did not inhibit the cold acclimation process, and the freezing stress experiment confirmed similar survival rates. The molecular analysis found distinct PPFD-specific adaptation mechanisms that were manifested in contrasting content of anthocyanins, cytokinin conjugates, abundances of proteins forming photosystems, and enzymes of protein, energy, and ROS metabolism pathways. Finally, this study led to the identification of putative proteins and metabolite markers correlating with susceptibility to freezing stress of non-acclimated plants grown under low PPFD. Our data show that Arabidopsis plants grown under short-day photoperiod can be fully cold-acclimated under limited light conditions, employing standard and PPFD-specific pathways.

2021-07-08 | PXD025234 | Pride

Gene expression in pif1pif3pif4pif5 mutant under dark or red light conditions

Project description:Light initiates the seedling deetiolation transition by promoting major changes in gene expression mainly regulated by phytochrome (phy) photoreceptors. During the initial dark-to-light transition, phy photoactivation induces rapid changes in gene expression that eventually lead to the photomorphogenic development. Recent reports indicate that this process is achieved by phy-induced degradation of Phy-Interacting bHLH transcription Factors (PIFs) PIF1, PIF3 PIF4 and PIF5, which are partly redundant constitutive repressors of photomorphogenesis that accumulate in darkness. In order to test whether light/phy-regulated gene expression occurs through these PIFs, we have performed whole-genome expression analysis in the pif1pif3pif4pif5 quadruple mutant (pifq). Wild-type and pifq mutant seeds were plated on GM medium without sucrose at room temperature. During this procedure the seeds were routinely exposed to white light (WL) for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness, induced to germinate with a 5-min red pulse (Rp) (46 μmol/m2/s) and then incubated in the dark for 3h at 21°C before exposure to a terminal 5-min far red pulse (FRp) (58 μmol/m2/s) to suppress pseudo-dark effects. Seeds were then placed in either dark (D) or constant red light (Rc) (6.7 μmol/ m2/s) at 21°C for 45h (2d-old seedlings). Alternatively, 2d-old dark-grown seedlings were treated with 1h of red light (R1) (7.5 μmol/m2/s). Seed samples were harvested after stratification (5d stratified seeds).

2009-10-31 | E-GEOD-17159 | biostudies-arrayexpress

Tocopherols in Sunflower Seedlings under Light and Dark Conditions.

Project description:The objective of this study was to evaluate the dynamics of tocopherols in cotyledons and radicles from sunflower seeds with high and low total tocopherol content, mainly in the α-tocopherol form, and from seeds with increased proportions of β-, γ-, and δ-tocopherol, both under dark and light conditions. Tocopherol content was measured every 24 h from 1 to 12 days after sowing. In all cases, the content of individual tocopherol forms in the cotyledons and radicles was reduced along the sampling period, which was more pronounced under light conditions. The presence of light had a slightly greater effect on α- and γ-tocopherol than on β- and δ-tocopherol. A marked light effect was also observed on total tocopherol content, with light promoting the reduction of tocopherol content in cotyledons and radicles. The study revealed only slight differences in the patterns of tocopherol losses in lines with different tocopherol profiles, both under dark and light conditions, which suggested that the partial replacement of α-tocopherol by other tocopherol forms had no great impact on the protection against oxidative damage in seedlings.

| S-EPMC4549572 | biostudies-other

Gene expression from Arabidopsis under high light conditions

Project description:We have investigated the genomic response of Arabidopsis cell suspension culture under high light. Our main goal has been twofold: first, to establish whether chloroplasts in Arabidopsis cell suspension culture are functional and, as such, can act as sensors of adverse external stimuli leading to the activation of genomic defence responses in a manner similar to that described in whole plants exposed to a wide range of environmental stresses and; second, to distinguish which of the ROS that would be probably generated in the chloroplasts is predominant. Our functional genomic analysis has led us to conclude that singlet oxygen is the major ROS in Arabidopsis cell suspension culture under high light stress and that singlet oxygen production is responsible for a genomic activation associated with the biosynthesis and signalling pathway of several phytohormones that ultimately triggers accelerated cell death.

2011-05-05 | GSE22671 | GEO

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