An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis

Thum, Karen E.; Shin, Michael J.; Gutiérrez, Rodrigo A.; Mukherjee, Indrani; Katari, Manpreet S.; Nero, Damion; Shasha, Dennis; Coruzzi, Gloria M.

doi:10.1186/1752-0509-2-31

Cited by 56 publications

(71 citation statements)

References 54 publications

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“…This suggests that it would be possible to reinterrogate all existing microarray experiments (where controls are appropriately timed with the treatment samples) to begin a systematic analysis of how different genotypic and environmental perturbations not frequently tested for circadian clock influences may in fact alter the clock. Given that Arabidopsis has a vast database of microarray experiments, this could provide unique biological insights into novel connections between the circadian clock and physiology (Grennan, 2006;Jen et al, 2006;Obayashi et al, 2007;Thum et al, 2008). Within our analysis of natural variation and circadian clock output, this approach identified significant links between the plant metabolome and circadian clock outputs.…”

Section: Discussionmentioning

confidence: 97%

“…Previous work using a single model genotype of Arabidopsis has indicated that the circadian clock may alter the regulation of plant metabolism (Harmer et al, 2000;Gutierrez et al, 2008;Fukushima et al, 2009). Our results suggest that natural variation in the plant metabolome is also intimately linked to natural variation in circadian clock outputs and that the relationship maybe bidirectional.…”

Section: Plant Metabolism and Circadian Clock Outputsmentioning

confidence: 99%

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Network Quantitative Trait Loci Mapping of Circadian Clock Outputs Identifies Metabolic Pathway-to-Clock Linkages in Arabidopsis

et al. 2011

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Modern systems biology permits the study of complex networks, such as circadian clocks, and the use of complex methodologies, such as quantitative genetics. However, it is difficult to combine these approaches due to factorial expansion in experiments when networks are examined using complex methods. We developed a genomic quantitative genetic approach to overcome this problem, allowing us to examine the function(s) of the plant circadian clock in different populations derived from natural accessions. Using existing microarray data, we defined 24 circadian time phase groups (i.e., groups of genes with peak phases of expression at particular times of day). These groups were used to examine natural variation in circadian clock function using existing single time point microarray experiments from a recombinant inbred line population. We identified naturally variable loci that altered circadian clock outputs and linked these circadian quantitative trait loci to preexisting metabolomics quantitative trait loci, thereby identifying possible links between clock function and metabolism. Using single-gene isogenic lines, we found that circadian clock output was altered by natural variation in Arabidopsis thaliana secondary metabolism. Specifically, genetic manipulation of a secondary metabolic enzyme led to altered free-running rhythms. This represents a unique and valuable approach to the study of complex networks using quantitative genetics.

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Section: Discussionmentioning

confidence: 97%

Section: Plant Metabolism and Circadian Clock Outputsmentioning

confidence: 99%

Network Quantitative Trait Loci Mapping of Circadian Clock Outputs Identifies Metabolic Pathway-to-Clock Linkages in Arabidopsis

et al. 2011

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“…The regulation of N uptake and assimilation is multifaceted and may involve N metabolite sensing and signaling mechanisms in shoot and root as well as shoot-to-root communication ( Fig. 6; Ruffel et al, 2008;Thum et al, 2008;Vidal and Gutiérrez, 2008;Ho et al, 2009;NunesNesi et al, 2010;Wang et al, 2012). Amino acids like Glu, Gln, or Asn have been shown to regulate the expression of genes involved in N uptake and assimilation (Cooper and Clarkson, 1989;Imsande and Touraine, 1994;Lam et al, 1998;Gutiérrez et al, 2008).…”

Section: Nue Is Greatly Improved In Aap1-oe Plantsmentioning

confidence: 99%

Improving Plant Nitrogen Use Efficiency through Alteration of Amino Acid Transport Processes

2017

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Improving the efficiency of nitrogen (N) uptake and utilization in plants could potentially increase crop yields while reducing N fertilization and, subsequently, environmental pollution. Within most plants, N is transported primarily as amino acids. In this study, pea (Pisum sativum) plants overexpressing AMINO ACID PERMEASE1 (AAP1) were used to determine if and how genetic manipulation of amino acid transport from source to sink affects plant N use efficiency. The modified plants were grown under low, moderate, or high N fertilization regimes. The results showed that, independent of the N nutrition, the engineered plants allocate more N via the vasculature to the shoot and seeds and produce more biomass and higher seed yields than wild-type plants. Dependent on the amount of N supplied, the AAP1-overexpressing plants displayed improved N uptake or utilization efficiency, or a combination of the two. They also showed significantly increased N use efficiency in N-deficient as well as in N-rich soils and, impressively, required half the amount of N to produce as many fruits and seeds as control plants. Together, these data support that engineering N allocation from source to sink presents an effective strategy to produce crop plants with improved productivity as well as N use efficiency in a range of N environments.Nitrogen (N) is an essential nutrient that plants require in large amounts for growth and development. In industrial countries, high N fertilization enables maximum crop yields, and in the last 50 years, the use of synthetic N fertilizers has increased dramatically to meet the agricultural demands of a growing population (FAO, 2012;Conant et al., 2013). However, depending on the crop species and soil conditions, plants take up less than half of the applied N fertilizer (Raun and Johnson, 1999;Hodge et al., 2000;Kumar and Goh, 2002;Yang et al., 2015;Zhu et al., 2016). The remaining soil N may contaminate aquatic systems through runoffs or leached water (Crews and Peoples, 2005;Gruber and Galloway, 2008) or it may undergo denitrification and be released into the atmosphere as nitrous oxide, a powerful greenhouse gas (Bouwman, 1996;Bouwman et al., 2002), altogether resulting in negative effects on the environment and human health. Oppositely, in developing countries, access to N fertilizer is limited, and insufficient N nutrition results in low crop productivity and, ultimately, in reduced food supply (Brown et al., 2009;Lal, 2009).One solution to these issues is the production of crop varieties that are highly efficient in using N and produce high yields with reduced N input (MasclauxDaubresse et al., 2010;McAllister et al., 2012;Garnett et al., 2015). Plant nitrogen use efficiency (NUE) is determined by plant seed yield relative to the amount of N applied and is generally composed of both N uptake and N utilization efficiency (Moll et al., 1982). Nitrogen uptake efficiency (NUpE) is defined as total shoot N relative to the amount of N supplied to the soil. The uptake of N by the root is influenced by th...

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“…et al, 2012). Several of the studies involving mutant lines that had similar profiles to grapevine buds (BioProject PRJNA327467) also related to light and carbon signaling, for example, a study of the role of the COP1 in coordinating light-dependent signaling (GEO accession GSE22983; Chang et al, 2011) and a study identifying CARBON AND LIGHT INSENSITIVE (CLI186) mutants (ArrayExpress accession E-MEXP-1112; Thum et al, 2008).…”

Section: Sugar Metabolism Is Regulated By Light At Early Stages Of Grmentioning

confidence: 99%

Roles for Light, Energy, and Oxygen in the Fate of Quiescent Axillary Buds

et al. 2017

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The hierarchy of events governing the resumption of growth of a quiescent axillary bud are poorly understood. During quiescence, a homeostasis exists in phytohormone and source/sink regulation, which represses the metabolic and mitotic progression of the bud. Environmental change and shoot development can alter the homeostasis, leading to a binary state change and the commitment to growth. Within this context, light and oxygen availability can serve both metabolic and signaling functions. However, the question of substrate versus signal has proven challenging to resolve; in the case of sugars, there are disparities in the data from apical and axillary buds in juvenile shoots, while in postdormant perennial buds, light has only a facultative role in the decision, but signaling may still be essential for bud fate. We briefly update the roles and hierarchies of light-, energy-, and oxygen-dependent functions in axillary bud outgrowth of annual shoots, before focusing discussion on the role of chloroplast-to-nucleus retrograde signaling genes such as GENOMES UNCOUPLED4 (GUN4) and ELONGATED HYPOCOTYL5 (HY5) in bud burst responses to light, examining available transcriptome data from postdormant grapevine (Vitis vinifera) buds. We discuss the evidence implicating cryptochromes (CRY) in the activation of HY5 expression in grapevine, leading to chloroplast biogenesis in the buds, and that

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An integrated genetic, genomic and systems approach defines gene networks regulated by the interaction of light and carbon signaling pathways in Arabidopsis

Cited by 56 publications

References 54 publications

Network Quantitative Trait Loci Mapping of Circadian Clock Outputs Identifies Metabolic Pathway-to-Clock Linkages in Arabidopsis

Network Quantitative Trait Loci Mapping of Circadian Clock Outputs Identifies Metabolic Pathway-to-Clock Linkages in Arabidopsis

Improving Plant Nitrogen Use Efficiency through Alteration of Amino Acid Transport Processes

Roles for Light, Energy, and Oxygen in the Fate of Quiescent Axillary Buds

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