Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsisrosettes

Gibon, Yves; Usadel, Björn; Blaesing, Oliver E.; Kamlage, Beate; Hoehne, Melanie; Trethewey, Richard N.; Stitt, Mark

doi:10.1186/gb-2006-7-8-r76

Cited by 302 publications

(141 citation statements)

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“…Osuna et al [19] reported changes in transcript levels for >1,700 genes after 3 h of 15 mM sucrose addition to Arabidopsis plants. A comprehensive analysis revealed radical changes at the metabolic, proteomic, and overall transcriptional levels during a circadian cycle and extended night in wild-type Arabidopsis plants and starchless pgm mutant [19, 22, 23]. Bläsing et al [20] showed that more than 17% of the genes presented more than a two-fold larger diurnal change in the starchless pgm mutant when compared with Col-0.…”

Section: Discussionmentioning

confidence: 99%

“…Thousands of genes showed significant transcript changes in Arabidopsis starchless mutants lacking the chloroplastic isoform of phosphoglucomutase (PGM) gene when compared with wild-type plants at different time-points during diurnal light/dark cycles [19, 22, 23]. Nevertheless, little is known about the proteome profiling in plant carbohydrate metabolism.…”

Section: Introductionmentioning

confidence: 99%

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Transcriptomic and proteomic approach to identify differentially expressed genes and proteins in Arabidopsis thaliana mutants lacking chloroplastic 1 and cytosolic FBPases reveals several levels of metabolic regulation

et al. 2016

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BackgroundDuring the photosynthesis, two isoforms of the fructose-1,6-bisphosphatase (FBPase), the chloroplastidial (cFBP1) and the cytosolic (cyFBP), catalyse the first irreversible step during the conversion of triose phosphates (TP) to starch or sucrose, respectively. Deficiency in cyFBP and cFBP1 isoforms provokes an imbalance of the starch/sucrose ratio, causing a dramatic effect on plant development when the plastidial enzyme is lacking.ResultsWe study the correlation between the transcriptome and proteome profile in rosettes and roots when cFBP1 or cyFBP genes are disrupted in Arabidopsis thaliana knock-out mutants. By using a 70-mer oligonucleotide microarray representing the genome of Arabidopsis we were able to identify 1067 and 1243 genes whose expressions are altered in the rosettes and roots of the cfbp1 mutant respectively; whilst in rosettes and roots of cyfbp mutant 1068 and 1079 genes are being up- or down-regulated respectively. Quantitative real-time PCR validated 100% of a set of 14 selected genes differentially expressed according to our microarray analysis. Two-dimensional (2-D) gel electrophoresis-based proteomic analysis revealed quantitative differences in 36 and 26 proteins regulated in rosettes and roots of cfbp1, respectively, whereas the 18 and 48 others were regulated in rosettes and roots of cyfbp mutant, respectively. The genes differentially expressed and the proteins more or less abundant revealed changes in protein metabolism, RNA regulation, cell signalling and organization, carbon metabolism, redox regulation, and transport together with biotic and abiotic stress. Notably, a significant set (25%) of the proteins identified were also found to be regulated at a transcriptional level.ConclusionThis transcriptomic and proteomic analysis is the first comprehensive and comparative study of the gene/protein re-adjustment that occurs in photosynthetic and non-photosynthetic organs of Arabidopsis mutants lacking FBPase isoforms.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0945-7) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Transcriptomic and proteomic approach to identify differentially expressed genes and proteins in Arabidopsis thaliana mutants lacking chloroplastic 1 and cytosolic FBPases reveals several levels of metabolic regulation

et al. 2016

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“…Several examples concerning the iron transporter IRT1 (57), the high-affinity NO 3 Ϫ transporter from Tuber borchii (58), the sulfate transporter HVST1 from barley (59), the phosphate transporter PT1 from Medicago and tomato (60,61), and aquaporines (62) all showed a correlation between the level of mRNA and the level of the protein in response to iron starvation, nitrogen availability, sulfate re-supply, phosphate starvation, and salinity, respectively. However, recent large-scale experiments showed that transcript levels undergo marked and rapid changes during diurnal cycles and after transfer to darkness, whereas changes in enzyme activities are smaller and delayed (63). This strongly suggests that in many cases additional regulation at the level of protein is required.…”

Section: Discussionmentioning

confidence: 99%

Regulation of Root Nitrate Uptake at the NRT2.1 Protein Level in Arabidopsis thaliana

Wirth

Chopin

Santoni

et al. 2007

Journal of Biological Chemistry

155

172

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In Arabidopsis the NRT2.1 gene encodes a main component of the root high-affinity nitrate uptake system (HATS). Its regulation has been thoroughly studied showing a strong correlation between NRT2.1 expression and HATS activity. Despite its central role in plant nutrition, nothing is known concerning localization and regulation of NRT2.1 at the protein level. By combining a green fluorescent protein fusion strategy and an immunological approach, we show that NRT2.1 is mainly localized in the plasma membrane of root cortical and epidermal cells, and that several forms of the protein seems to co-exist in cell membranes (the monomer and at least one higher molecular weight complex). The monomer is the most abundant form of NRT2.1, and seems to be the one involved in NO 3 ؊ transport. It strictly requires the NAR2.1 protein to be expressed and addressed at the plasma membrane. No rapid changes in NRT2.1 abundance were observed in response to light, sucrose, or nitrogen treatments that strongly affect both NRT2.1 mRNA level and HATS activity. This suggests the occurrence of posttranslational regulatory mechanisms. One such mechanism could correspond to the cleavage of NRT2.1 C terminus, which results in the presence of both intact and truncated proteins in the plasma membrane.The NRT2.1 gene of Arabidopsis thaliana is part of a small multigene family comprising 7 members, which with the exception of NRT2.7, are predominantly expressed in the roots (1, 2). NRT2 genes are found in a large variety of organisms (fungi, certain yeasts, green algae, and plants) and belong to the nitrate nitrite porter family of transporter genes (3).It is generally assumed that NRT2 genes encode high-affinity nitrate (NO 3 Ϫ ) or nitrite transporters (4 -11), and that in higher plants, they play a key role in the root high-affinity transport system (HATS), 3 which ensures uptake of NO 3 Ϫ from the soil solution (3,(12)(13)(14). In all plant species investigated to date, the NO 3 Ϫ HATS displays a saturable activity, with a V max generally reached for NO 3 Ϫ concentrations comprised between 0.2 and 0.5 mM (3,12,14). Although the functional characterization of almost all higher plant NRT2 transporters remains to be done, it is now well documented that NRT2.1 is a major component of the HATS in A. thaliana as shown by the fact that (i) of the seven NRT2 members, only NRT2.1 transcript abundance showed significant correlation (r 2 ϭ 0.74) with HATS activity (2, 11) and (ii) several mutants disrupted for the NRT2.1 gene (15, 16) or for both NRT2.1-NRT2.2 genes (17, 18) have lost up to 75% of the high-affinity NO 3 Ϫ uptake activity. As a consequence, growth of these mutants is severely impaired at low NO 3 Ϫ concentration (15,19,20), but not at high NO 3 Ϫ concentration when low-affinity transporters, most probably those of the NRT1 family (3,12,14), are active.Despite its firmly established role in root NO 3 Ϫ uptake, several aspects of NRT2.1 function remain enigmatic. First, unlike the Aspergillus nidulans or Chlorella sorokiniana NRT2 trans...

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“…The resulting energy deprivation was suggested to be common to most types of stress and to trigger specific responses (Baena-González and Sheen, 2008), leading to the massive alteration of cellular processes, referred to as LES. This includes growth arrest and metabolic reprogramming, comprising the repression of biosynthetic activities and sugar storage, as well as the induction of catabolic processes, photosynthesis, and sugar remobilization (Paul and Pellny, 2003; Gibon et al, 2006). In addition, the expression of thousands of genes is altered (Usadel et al, 2008).…”

Section: The Low Energy Syndrome Is Part Of Stress Adaptationmentioning

confidence: 99%

The low energy signaling network

et al. 2014

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Stress impacts negatively on plant growth and crop productivity, caicultural production worldwide. Throughout their life, plants are often confronted with multiple types of stress that affect overall cellular energy status and activate energy-saving responses. The resulting low energy syndrome (LES) includes transcriptional, translational, and metabolic reprogramming and is essential for stress adaptation. The conserved kinases sucrose-non-fermenting-1-related protein kinase-1 (SnRK1) and target of rapamycin (TOR) play central roles in the regulation of LES in response to stress conditions, affecting cellular processes and leading to growth arrest and metabolic reprogramming. We review the current understanding of how TOR and SnRK1 are involved in regulating the response of plants to low energy conditions. The central role in the regulation of cellular processes, the reprogramming of metabolism, and the phenotypic consequences of these two kinases will be discussed in light of current knowledge and potential future developments.

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Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsisrosettes

Cited by 302 publications

References 63 publications

Transcriptomic and proteomic approach to identify differentially expressed genes and proteins in Arabidopsis thaliana mutants lacking chloroplastic 1 and cytosolic FBPases reveals several levels of metabolic regulation

Transcriptomic and proteomic approach to identify differentially expressed genes and proteins in Arabidopsis thaliana mutants lacking chloroplastic 1 and cytosolic FBPases reveals several levels of metabolic regulation

Regulation of Root Nitrate Uptake at the NRT2.1 Protein Level in Arabidopsis thaliana

The low energy signaling network

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