Use of transcriptomics and co-expression networks to analyze the interconnections between nitrogen assimilation and photorespiratory metabolism

Pérez-Delgado, Carmen M.; Moyano, Tomás C.; García‐Calderón, Margarita; Canales, Javier; Gutiérrez, Rodrigo A.; Márquez, Antonio J.; Betti, Marco

doi:10.1093/jxb/erw170

Cited by 26 publications

(23 citation statements)

References 74 publications

(107 reference statements)

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“…The Ljgln2-2 mutant is able to grow in a similar manner to the wild-type (WT) at high CO 2 conditions that suppress PR. However, it accumulates high levels of NH 4 + when transferred from high CO 2 to air conditions, as a consequence of the activation of PR and the lack of GS 2 (Orea et al 2002, Pérez-Delgado et al 2013, Betti et al 2014, Pérez-Delgado et al 2015. Photorespiratory ammonium accumulation was also shown previously in barley GS 2 mutants (Wallsgrove et al 1987) and in GS 2 -antisense oilseed rape lines (Husted et al 2002).…”

Section: Introductionsupporting

confidence: 59%

“…The first GS photorespiratory mutants isolated from legume plants were identified several years ago in our laboratory from the model legume L. japonicus (Orea et al 2002, Márquez et al 2005). These mutants have been substantially characterized at the molecular and physiological levels (Orea et al 2002, Márquez et al 2005, Betti et al 2006, Pérez-Delgado et al 2013, Betti et al 2014, Pérez-Delgado et al 2016. One of the mutants, named Ljgln2-2, is deficient in plastidic GS (GS 2 ) but has normal levels of cytosolic GS (GS 1 ) (Orea et al 2002, Márquez et al 2005, Betti et al 2012.…”

Section: Introductionmentioning

confidence: 99%

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The afterglow thermoluminescence band as an indicator of changes in the photorespiratory metabolism of the model legumeLotus japonicus

García‐Calderón

Betti

Márquez

et al. 2019

Physiologia Plantarum

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The afterglow (AG) luminescence is a delayed chlorophyll fluorescence emitted by the photosystem II that seems to reflect the level of assimilatory potential (NADPH+ATP) in chloroplast. In this work, the thermoluminescence (TL) emissions corresponding to the AG band were investigated in plants of the WT and the Ljgln2‐2 photorespiratory mutant from Lotus japonicus grown under either photorespiratory (air) or non‐photorespiratory (high concentration of CO2) conditions. TL glow curves obtained after two flashes induced the strongest overall TL emissions, which could be decomposed in two components: B band (tmax = 27–29°C) and AG band (tmax = 44–45°C). Under photorespiratory conditions, WT plants showed a ratio of 1.17 between the intensity of the AG and B bands (IAG/IB). This ratio increased considerably under non‐photorespiratory conditions (2.12). In contrast, mutant Ljgln2‐2 plants grown under both conditions showed a high IAG/IB ratio, similar to that of WT plants grown under non‐photorespiratory conditions. In addition, high temperature thermoluminescence (HTL) emissions associated to lipid peroxidation were also recorded. WT and Ljgln2‐2 mutant plants grown under photorespiratory conditions showed both a significant HTL band, which increased significantly under non‐photorespiratory conditions. The results of this work indicate that changes in the amplitude of IAG/IB ratio could be used as an in vivo indicator of alteration in the level of photorespiratory metabolism in L. japonicus chloroplasts. Moreover, the HTL results suggest that photorespiration plays some role in the protection of the chloroplast against lipid peroxidation.

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Section: Introductionsupporting

confidence: 59%

Section: Introductionmentioning

confidence: 99%

The afterglow thermoluminescence band as an indicator of changes in the photorespiratory metabolism of the model legumeLotus japonicus

García‐Calderón

Betti

Márquez

et al. 2019

Physiologia Plantarum

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“…WGCNA identifies clusters (modules) of highly co-expressed genes based on gene expression similarity, and has been demonstrated to identify important genes associated with complex phenotypes and biological processes in plants 33–35 . We identified 10 gene modules (designated M1–M10; capturing 8,525 genes) (Fig.…”

Section: Resultsmentioning

confidence: 99%

A systems approach to a spatio-temporal understanding of the drought stress response in maize

Miao

Han

Zhang

et al. 2017

Sci Rep

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Crops are often subjected to periods of drought stress during their life cycle. However, how stress response mechanisms contribute to the crosstalk between stress signaling pathways and developmental signaling pathways is still unknown. We built a gene co-expression network from a spatio-temporal transcriptomic map of the drought stress response in maize (Zea mays), profiled from three tissues and four developmental stages and characterized hub genes associated with duplication events, selection, and regulatory networks. Co-expression analysis grouped drought-response genes into ten modules, covering 844 highly connected genes (hub genes). Of these, 15.4% hub genes had diverged by whole-genome duplication events and 2.5% might then have been selected during natural domestication and artificial improvement processes, successively. We identified key transcription factor hubs in a transcriptional regulatory network, which may function as a crosstalk mechanism between drought stress and developmental signalling pathways in maize. Understanding the evolutionary biases that have evolved to enhance drought adaptation lays the foundation for further dissection of crosstalk between stress signalling pathways and developmental signalling pathways in maize, towards molecular design of new cultivars with desirable yield and greater stress tolerance.

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“…Thus, the C : N regulation mechanism allows plants to activate genes involved in N assimilation when C skeletons are abundant and internal organic N levels are low, or disrupt N uptake when photosynthesis levels are low or the internal organic N levels are high (Coruzzi and Zhou, 2001). Carbon metabolism influences N metabolism and vice versa (Pé rez-Delgado et al, 2016). Plants can develop mechanisms to detect the N status of the root system and soil and, thus, coordinate responses in their leaves that will influence photosynthetic yield (Elser et al, 2010;Pé rez-Delgado et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

“…Carbon metabolism influences N metabolism and vice versa (Pé rez-Delgado et al, 2016). Plants can develop mechanisms to detect the N status of the root system and soil and, thus, coordinate responses in their leaves that will influence photosynthetic yield (Elser et al, 2010;Pé rez-Delgado et al, 2016). Based on DRIS analyses, nitrogen was the most limiting nutrient to plant growth in competition (Tab.…”

Section: Discussionmentioning

confidence: 99%

Interspecific competition changes nutrient : nutrient ratios of weeds and maize

Matos

Teixeira

Silva

et al. 2019

J. Plant Nutr. Soil Sci.

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The elemental ratios of plant tissues are associated with the adaptive and competitive success of a plant species in an ecosystem. So far, no study has evaluated if and how crop–weed competition influences the elemental ratios of competing populations, although such information is important to understand weed infestation dynamics and to improve weed management in agroecosystems. The objective of this study was to analyze weed–crop elemental ratios during interspecific competition between weeds and crops in greenhouse experiments. For this, maize (Zea mays L.) and the weeds Amaranthus viridis L, Bidens pilosa L., and Ipomoea grandifolia (Dammer) O'Donell were grown under seven treatments: maize and weed monocultures, and maize in competition with weeds. Competition between plants practically did not influence growth and nutrient contents of maize but reduced weed growth and nutrient uptake. Maize showed few changes in elemental ratios. In contrast, B. pilosa and I. grandifolia were very sensitive to competition and showed significant increases in C : N, C : P, C : K, N : P, and N : K ratios when grown with maize. A. viridis showed low flexibility of nutrient : nutrient ratios under the same competitive pressure as that faced by B. pilosa and I. grandifolia. The interspecific competition led to increases only in the C : P ratio of A. viridis shoots. Therefore, interspecific competition changes the elemental ratios, mainly of the weeds, and the magnitude of this change is dependent on the plant species involved. Interspecific competition changes plant biomass quality (higher C : nutrient ratios), mainly for B. pilosa and I. grandifolia.

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Use of transcriptomics and co-expression networks to analyze the interconnections between nitrogen assimilation and photorespiratory metabolism

Abstract: HighlightA clear interconnection between photorespiration and primary nitrogen assimilation is established in Lotus japonicus, and key transcription factors connected to both routes are identified using transcriptomics and gene co-expression networks.

Cited by 26 publications

References 74 publications

The afterglow thermoluminescence band as an indicator of changes in the photorespiratory metabolism of the model legumeLotus japonicus

The afterglow thermoluminescence band as an indicator of changes in the photorespiratory metabolism of the model legumeLotus japonicus

A systems approach to a spatio-temporal understanding of the drought stress response in maize

Interspecific competition changes nutrient : nutrient ratios of weeds and maize

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