ArticleBMC systems biology2008
An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis.
Article in BMC systems biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 59 citations in OpenAlex.
- Current Challenges in Plant Systems Biology.Advances in experimental medicine and biology · 2021Article
- Improving coordination of plant growth and nitrogen metabolism for sustainable agriculture.aBIOTECH · 2020Review
- SDG8-Mediated Histone Methylation and RNA Processing Function in the Response to Nitrate Signaling.Plant physiology · 2020Article
- ThePlant direct · 2019Article
- Roles for Light, Energy, and Oxygen in the Fate of Quiescent Axillary Buds.Plant physiology · 2018Review
- Construction of a network describing asparagine metabolism in plants and its application to the identification of genes affecting asparagine metabolism in wheat under drought and nutritional stress.Food and energy security · 2018Article
- Improving Plant Nitrogen Use Efficiency through Alteration of Amino Acid Transport Processes.Plant physiology · 2017Article
- QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability.Omics : a journal of integrative biology · 2015Review
- HY5 regulates nitrite reductase 1 (NIR1) and ammonium transporter1;2 (AMT1;2) in Arabidopsis seedlings.Plant science : an international journal of experimental plant biology · 2015Article
- The histone methyltransferase SDG8 mediates the epigenetic modification of light and carbon responsive genes in plants.Genome biology · 2015Article
- The QQS orphan gene of Arabidopsis modulates carbon and nitrogen allocation in soybean.Plant biotechnology journal · 2015Article
- Identification of gene functions associated to active and dormant buds in Arabidopsis.Plant signaling & behavior · 2014Article
- From dusk till dawn: the Arabidopsis thaliana sugar starving responsive network.Frontiers in plant science · 2014Article
- Article
- Prediction of biological functions of Shewanella-like protein phosphatases (Shelphs) across different domains of life.Functional & integrative genomics · 2012Review
- Article
- Network quantitative trait loci mapping of circadian clock outputs identifies metabolic pathway-to-clock linkages in Arabidopsis.The Plant cell · 2011Article
- SLocX: Predicting Subcellular Localization of Arabidopsis Proteins Leveraging Gene Expression Data.Frontiers in plant science · 2011Article
- Individual vs. combinatorial effect of elevated CO2 conditions and salinity stress on Arabidopsis thaliana liquid cultures: comparing the early molecular response using time-series transcriptomic and metabolomic analyses.BMC systems biology · 2010Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundLight and carbon are two important interacting signals affecting plant growth and development. The mechanism(s) and/or genes involved in sensing and/or mediating the signaling pathways involving these interactions are unknown. This study integrates genetic, genomic and systems approaches to identify a genetically perturbed gene network that is regulated by the interaction of carbon and light signaling in Arabidopsis.
resultsCarbon and light insensitive (cli) mutants were isolated. Microarray data from cli186 is analyzed to identify the genes, biological processes and gene networks affected by the integration of light and carbon pathways. Analysis of this data reveals 966 genes regulated by light and/or carbon signaling in wild-type. In cli186, 216 of these light/carbon regulated genes are misregulated in response to light and/or carbon treatments where 78% are misregulated in response to light and carbon interactions. Analysis of the gene lists show that genes in the biological processes "energy" and "metabolism" are over-represented among the 966 genes regulated by carbon and/or light in wild-type, and the 216 misregulated genes in cli186. To understand connections among carbon and/or light regulated genes in wild-type and the misregulated genes in cli186, the microarray data is interpreted in the context of metabolic and regulatory networks. The network created from the 966 light/carbon regulated genes in wild-type, reveals that cli186 is affected in the light and/or carbon regulation of a network of 60 connected genes, including six transcription factors. One transcription factor, HAT22 appears to be a regulatory "hub" in the cli186 network as it shows regulatory connections linking a metabolic network of genes involved in "amino acid metabolism", "C-compound/carbohydrate metabolism" and "glycolysis/gluconeogenesis".
conclusionThe global misregulation of gene networks controlled by light and carbon signaling in cli186 indicates that it represents one of the first Arabidopsis mutants isolated that is specifically disrupted in the integration of both carbon and light signals to control the regulation of metabolic, developmental and regulatory genes. The network analysis of misregulated genes suggests that CLI186 acts to integrate light and carbon signaling interactions and is a master regulator connecting the regulation of a host of downstream metabolic and regulatory processes.
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