Ontology highlight
ABSTRACT:
PROVIDER: PRJNA887392 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21814500_1.fastq.gz | Fastqsanger.gz | |||
| SRR21814500_2.fastq.gz | Fastqsanger.gz | |||
| SRR21814501_1.fastq.gz | Fastqsanger.gz | |||
| SRR21814501_2.fastq.gz | Fastqsanger.gz | |||
| SRR21814502_1.fastq.gz | Fastqsanger.gz |
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Project description:deOliveiraDalMolin2010 - Genome-scale
metabolic network of Arabidopsis thaliana (AraGEM)
This model is described in the article:
AraGEM, a genome-scale
reconstruction of the primary metabolic network in
Arabidopsis.
de Oliveira Dal'Molin CG, Quek LE,
Palfreyman RW, Brumbley SM, Nielsen LK.
Plant Physiol. 2010 Feb; 152(2):
579-589
Abstract:
Genome-scale metabolic network models have been successfully
used to describe metabolism in a variety of microbial organisms
as well as specific mammalian cell types and organelles. This
systems-based framework enables the exploration of global
phenotypic effects of gene knockouts, gene insertion, and
up-regulation of gene expression. We have developed a
genome-scale metabolic network model (AraGEM) covering primary
metabolism for a compartmentalized plant cell based on the
Arabidopsis (Arabidopsis thaliana) genome. AraGEM is a
comprehensive literature-based, genome-scale metabolic
reconstruction that accounts for the functions of 1,419 unique
open reading frames, 1,748 metabolites, 5,253 gene-enzyme
reaction-association entries, and 1,567 unique reactions
compartmentalized into the cytoplasm, mitochondrion, plastid,
peroxisome, and vacuole. The curation process identified 75
essential reactions with respective enzyme associations not
assigned to any particular gene in the Kyoto Encyclopedia of
Genes and Genomes or AraCyc. With the addition of these
reactions, AraGEM describes a functional primary metabolism of
Arabidopsis. The reconstructed network was transformed into an
in silico metabolic flux model of plant metabolism and
validated through the simulation of plant metabolic functions
inferred from the literature. Using efficient resource
utilization as the optimality criterion, AraGEM predicted the
classical photorespiratory cycle as well as known key
differences between redox metabolism in photosynthetic and
nonphotosynthetic plant cells. AraGEM is a viable framework for
in silico functional analysis and can be used to derive new,
nontrivial hypotheses for exploring plant metabolism.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180028.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
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To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
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Public Domain Dedication for more information.
2015-07-30 | MODEL1507180028 | BioModels
Project description:It has been reported that a number of small coding genes (30–100 amino acids) tend to be lineage-specifically emerged in evolution but such de-novo genes tend to be missed in genomes. Plant mitochondrial genomes might be fostering sources of de-novo genes because of a high rearrangement rate. However, the functional role of de-novo genes derived from mitochondria is unclear. Here, in the best model species of plants (Arabidopsis thaliana), we showed that Arabidopsis-specifically emerged de-novo genes derived from mitochondrial genome contributed to phenotypic variation in a species. We previously identified 49 candidates of small coding genes inducing abnormal morphological changes on overexpression in the nuclear genome. Among them, we focused on a candidate (sORF2146) potentially encoding 66 amino acids in large-scale intergenic genomic transferring region from mitochondrial genome. Comparative genome analysis showed that sORF2146 had been appeared in Arabidopsis lineage. Mitochondrial sORF2146 is fixed among A. thaliana ecotypes but nucleus sORF2146 is not fixed in A. thaliana ecotypes. After showing evidence that nucleus sORF2146 was transcribed and translated as a coding gene, we performed transcriptome analysis in transgenic plant overexpressing sORF2146. Genes associated with flowering transition are highly regulated in the transgenic plant. We then examined phenotypic effects of overexpression and knockdown transgenic plant. Overexpression and knockdown transgenic plant induce late and early flowering, respectively. Taken together, we conclude that a nucleus de-novo gene derived from mitochondria contributes to the variation of floral timing in Arabidopsis population.
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