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Dirk Inze

Ghent University, VIB Department of Plant Systems Biology, Faculty Member

VIB, Department of Plant Systems Biology, Faculty Member

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Central Research Institute for Dryland Agriculture

Jameel M Al-Khayri

King Faisal University

INDIAN AGRICULTURAL RESEARCH INSTITUTE, NEW DELHI, INDIA

Istanbul University

Professor Bashir O M O L A R A N Bello

University of Abuja, Nigeria

Naorem Brajendra Singh

Central Agricultural University (CAU), Imphal

Slovak University of Agriculture (SPU)

Prof.Dr. Hakan Ulukan

Ankara

North Carolina State University

Prof Manjit S Kang

Kansas State University

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Papers by Dirk Inze

Regulation of Cell Division in Arabidopsis

by Dirk Inze and Orit Shaul

Critical Reviews in Plant Sciences, 1996

The study of cell cycle control in plants is expected to contribute to the understanding of plant... more The study of cell cycle control in plants is expected to contribute to the understanding of plants&amp;amp;#39; unique developmental features. The principal regulators of the eukaryotic cell cycle, namely, cyclin-dependent kinases (CDKs) and cyclins, are also conserved in plants. This review is concerned with our present knowledge on cell cycle regulation in Arabidopsis thaliana, which is widely accepted as a

Cloning and characterization of a novel Mg2+/H+ exchanger

by Dirk Inze, Orit Shaul, Gad Galili, and Janice Engler

The EMBO Journal, 1999

Cellular functions require adequate homeostasis of several divalent metal cations, including Mg2+... more Cellular functions require adequate homeostasis of several divalent metal cations, including Mg2+ and Zn2+. Mg2+, the most abundant free divalent cytoplasmic cation, is essential for many enzymatic reactions, while Zn2+ is a structural constituent of various enzymes. Multicellular organisms have to balance not only the intake of Mg2+ and Zn2+, but also the distribution of these ions to various organs. To date, genes encoding Mg2+ transport proteins have not been cloned from any multicellular organism. We report here the cloning and characterization of an Arabidopsis thaliana transporter, designated AtMHX, which is localized in the vacuolar membrane and functions as an electrogenic exchanger of protons with Mg2+ and Zn2+ ions. Functional homologs of AtMHX have not been cloned from any organism. Ectopic overexpression of AtMHX in transgenic tobacco plants render them sensitive to growth on media containing elevated levels of Mg2+ or Zn2+, but does not affect the total amounts of these minerals in shoots of the transgenic plants, AtMHX mRNA is mainly found at the vascular cylinder, and a large proportion of the mRNA is localized in close association with the xylem tracheary elements. This localization suggests that AtMHX may control the partitioning of Mg2+ and Zn2+ between the various plant organs.

Cell Cycle Control in Arabidopsis

by Dirk Inze and Orit Shaul

Although the basic mechanism of cell cycle control is conserved among eukaryotes, its regulation ... more Although the basic mechanism of cell cycle control is conserved among eukaryotes, its regulation differs in each type of organism. Plants have unique developmental features that distinguish them from other eukaryotes. These include the absence of cell migration, the formation of organs throughout the entire life-span from specialized regions called meristems, and the potency of non-dividing cells to re-enter the cell cycle. The study of plant cell cycle control genes is expected to contribute to the understanding of these unique developmental phenomena. The principal regulators of the eukaryotic cell cycle, the cyclin-dependent kinases (CDKs) and cyclins, are conserved in plants. This review focuses on cell cycle regulation in the plant Arabidopsis thaliana. While expression of one Arabidopsis CDK gene, Cdc2aAt, was positively correlated with the competence of cells to divide, expression of a mitotic-like cyclin, cyc1At, was almost exclusively confined to dividing cells. The expression of the Arabidopsis δ-type cyclins appears to be an early stage in the response of plant cells to external and internal stimuli.

Levels of endogenous cytokinins, indole-3-acetic acid and abscisic acid during the cell cycle of synchronized tobacco BY-2 cells

by Orit Shaul and Dirk Inze

FEBS Letters, 1996

... FEBS 17337 FEBS Letters 391 (1996) 175180 Levels of endogenous cytokinins, indole3acetic acid... more

Two Arabidopsis Cyclin Promoters Mediate Distinctive Transcriptional Oscillation in Synchronized Tobacco BY2 Cells

by Sylvia Burssens, Vladimir Mironov, Orit Shaul, Dirk Inze, and Marc. Van Montagu

Proceedings of The National Academy of Sciences, 1996

Cyclins are cell cycle regulators whose proteins oscillate dramatically during the cell cycle. Cy... more Cyclins are cell cycle regulators whose proteins oscillate dramatically during the cell cycle. Cyclin steady-state mRNA levels also fluctuate, and there are indications that both their rate of transcription and mRNA stability are under cell cycle control. Here, we demonstrate the transcriptional regulation of higher eukaryote cyclins throughout the whole cell cycle with a high temporal resolution. The promoters of

A comprehensive analysis of hydrogen peroxide-induced gene expression in tobacco

by Luit Slooten, Dirk Inze, and Frank Breusegem

Proceedings of The National Academy of Sciences, 2003

Hydrogen peroxide plays a central role in launching the defense response during stress in plants.... more Hydrogen peroxide plays a central role in launching the defense response during stress in plants. To establish a molecular profile provoked by a sustained increase in hydrogen peroxide levels, catalase-deficient tobacco plants (CAT1AS) were exposed to high light (HL) intensities over a detailed time course. The expression kinetics of >14,000 genes were monitored by using transcript profiling technology based on cDNA-amplified fragment length polymorphism. Clustering and sequence analysis of 713 differentially expressed transcript fragments revealed a transcriptional response that mimicked that reported during both biotic and abiotic stresses, including the up-regulation of genes involved in the hypersensitive response, vesicular transport, posttranscriptional processes, biosynthesis of ethylene and jasmonic acid, proteolysis, mitochondrial metabolism, and cell death, and was accompanied by a very rapid up-regulation of several signal transduction components. Expression profiling corroborated by functional experiments showed that HL induced photoinhibition in CAT1AS plants and that a short-term HL exposure of CAT1AS plants triggered an increased tolerance against a subsequent severe oxidative stress.

Metabolic engineering of plant cell cultures - towards the new resources of alkaloids

Planta Medica Vol.72 Nr.11, 1031 54th Annual Congress on Medicinal Plant Research. Helsinki, Finl... more

Analysis of the spatial expression pattern of seven Kip related proteins (KRPs) in the shoot apex of Arabidopsis thaliana

Annals of Botany

Kip-related-proteins (KRPs), negative regulators of cell division, have recently been discovered ... more Kip-related-proteins (KRPs), negative regulators of cell division, have recently been discovered in plants but their in planta function is as yet unclear. In this study the spatial expression of all seven KRP genes in shoot apices of Arabidopsis thaliana were compared. In situ hybridization analyses were performed on longitudinal sections of shoot apices from 2-month-old Arabidopsis plants. The study provides evidence for different expression pattern groups. KRP1 and KRP2 expression is restricted to the endoreduplicating tissues. In contrast, KRP4 and KRP5 expression is mainly restricted to mitotically dividing cells. KRP3, KRP6 and KRP7 can be found in both mitotically dividing and endoreduplicating cells. The results suggest differential roles for the distinct KRPs. KRP1 and KRP2 might specifically be involved in the establishment of polyploidy. In contrast, KRP4 and KRP5 might be involved in regulating the progression through the mitotic cell cycle. KRP3, KRP6 and KRP7 might have...

Systems analysis of the responses to long-term magnesium deficiency and restoration in Arabidopsis thaliana

New Phytologist

*Unravelling mechanisms that control plant growth as a function of nutrient availability presents... more *Unravelling mechanisms that control plant growth as a function of nutrient availability presents a major challenge in plant biology. This study reports the first transcriptome response to long-term (1 wk) magnesium (Mg) depletion and restoration in Arabidopsis thaliana. *Before the outbreak of visual symptoms, genes responding to Mg starvation and restoration were monitored in the roots and young mature leaves and compared with the Mg fully supplied as control. *After 1 wk Mg starvation in roots and leaves, 114 and 2991 genes were identified to be differentially regulated, respectively, which confirmed the later observation that the shoot development was more affected than the root in Arabidopsis. After 24 h of Mg resupply, restoration was effective for the expression of half of the genes altered. We emphasized differences in the expression amplitude of genes associated with the circadian clock predominantly in leaves, a higher expression of genes in the ethylene biosynthetic pathw...

Low magnesium status in plants enhances tolerance to cadmium exposure

New Phytologist

In a transcriptomic study of magnesium (Mg) starvation in Arabidopsis, we identified several gene... more In a transcriptomic study of magnesium (Mg) starvation in Arabidopsis, we identified several genes that were differentially regulated which are involved in the detoxification process of nonessential heavy metals such as cadmium (Cd). We further tested the impact of low Mg status on Cd sensitivity in plants. Interestingly, a -Mg pretreatment of 7 d alleviated the bleaching of young leaves caused by Cd. No or little difference in Cd tissue concentration between the +Mg and -Mg plants was observed, suggesting that lower Cd toxicity was probably not attributable to modified root to shoot translocation. Mg deficiency also promoted an increase in the iron (Fe) concentration (up to one-fourth) in Cd-treated leaves. Because high Fe concentrations have previously been reported to prevent the harmful effects of Cd, we explored whether Fe homeostasis plays a role in the Mg-Cd interaction. A protective effect of -Mg pretreatment was also observed on Fe starvation. However, Fe foliar spray parti...

Early transcriptomic changes induced by magnesium deficiency in Arabidopsis thaliana reveal the alteration of circadian clock gene expression in roots and the triggering of abscisic acid-responsive genes

New Phytologist

*Plant growth and development ultimately depend on environmental variables such as the availabili... more *Plant growth and development ultimately depend on environmental variables such as the availability of essential minerals. Unravelling how nutrients affect gene expression will help to understand how they regulate plant growth. *This study reports the early transcriptomic response to magnesium (Mg) deprivation in Arabidopsis. Whole-genome transcriptome was studied in the roots and young mature leaves 4, 8 and 28 h after the removal of Mg from the nutrient solution. *The highest number of regulated genes was first observed in the roots. Contrary to other mineral deficiencies, Mg depletion did not induce a higher expression of annotated genes in Mg uptake. Remarkable responses include the perturbation of the central oscillator of the circadian clock in roots and the triggering of abscisic acid (ABA) signalling, with half of the up-regulated Mg genes in leaves being ABA-responsive. However, no change in ABA content was observed. *The specificity of the response of some Mg-regulated gen...

cell cycle interactome cytoscape file

cell cycle interactome excel file

Expression of a novel-type small proline-rich protein gene of alfalfa is induced by 2,4-dichlorophenoxiacetic acid in dedifferentiated callus cells

Plant molecular biology, 1997

Differential screening of a cDNA library of 2,4-dichlorophenoxiacetic acid (2,4-D)-treated alfalf... more Differential screening of a cDNA library of 2,4-dichlorophenoxiacetic acid (2,4-D)-treated alfalfa (Medicago sativa) callus tissues resulted in the isolation of a 571 bp cDNA clone (MsPRP5) encoding for a proline-rich protein (84 amino acids) with a specific repeat unit of TPVLPPRK/RGRPPPVPP. In addition, a characteristic amino acid block (PPVYK) previously found in other proline-rich proteins also occurs in the C-terminal region of MsPRP5. At the N-terminal, a signal peptide similar to leader sequences of extracellular proteins can be predicted. According to the northern analysis, the corresponding gene is not expressed or is weakly expressed in differentiated vegetative organs and somatic embryos. However the accumulation of MsPRP5 mRNA is auxin concentration-dependent in dedifferentiated callus tissue. An increase in the amount of steady-state mRNA was detected already 20 min after auxin shock (100 microM 2,4-D). Maximum expression was observed at 24-48 h in the presence of 2,4-D...

Changes in hydrogen peroxide homeostasis trigger an active cell death process in tobacco

In transgenic tobacco plants with reduced catalase activity, high levels of hydrogen peroxide (H ... more In transgenic tobacco plants with reduced catalase activity, high levels of hydrogen peroxide (H 2 O 2 ) can accumulate under photorespiratory conditions. Such a perturbation in H 2 O 2 homeostasis induced cell death in clusters of palisade parenchyma cells, primarily along the veins. Ultrastructural alterations, such as chromatin condensation and disruption of mitochondrial integrity, took place before cell death. Furthermore, enhanced transcript levels of mitochondrial defense genes accompanied these mitochondrial changes. Pharmacological data indicated that the initiation and execution of cell death require de novo protein synthesis and that the signal transduction pathway leading to cell death involved changes in ion homeostasis, (de)phosphorylation events and an oxidative burst, as observed during hypersensitive responses. This oxidase-dependent oxidative burst is essential for cell death, but it is not required for the accumulation of defense proteins, suggesting a more prominent role for the oxidative burst in abiotic stress-induced cell death.

Mass spectrometry-based sequencing of lignin oligomers

Plant physiology, 2010

Although the primary structure of proteins, nucleic acids, and carbohydrates can be readily deter... more Although the primary structure of proteins, nucleic acids, and carbohydrates can be readily determined, no sequencing method has been described yet for the second most abundant biopolymer on earth (i.e. lignin). Within secondary-thickened plant cell walls, lignin forms an aromatic mesh arising from the combinatorial radical-radical coupling of monolignols and many other less abundant monomers. This polymerization process leads to a plethora of units and linkage types that affect the physicochemical characteristics of the cell wall. Current methods to analyze the lignin structure focus only on the frequency of the major monomeric units and interunit linkage types but do not provide information on the presence of less abundant unknown units and linkage types, nor on how linkages affect the formation of neighboring linkages. Such information can only be obtained using a sequencing approach. Here, we describe, to our knowledge for the first time, a sequencing strategy for lignin oligome...

The elongata mutants identify a functional Elongator complex in plants with a role in cell proliferation during organ growth

Proceedings of The National Academy of Sciences, 2005

The key enzyme for transcription of protein-encoding genes in eukaryotes is RNA polymerase II (RN... more The key enzyme for transcription of protein-encoding genes in eukaryotes is RNA polymerase II (RNAPII). The recruitment of this enzyme during transcription initiation and its passage along the template during transcription elongation is regulated through the association and dissociation of several complexes. Elongator is a histone acetyl transferase complex, consisting of six subunits (ELP1-ELP6), that copurifies with the elongating RNAPII

The cyclin-dependent kinase inhibitor KRP6 induces mitosis and impairs cytokinesis in giant cells induced by plant-parasitic nematodes in Arabidopsis

In Arabidopsis thaliana, seven cyclin-dependent kinase (CDK) inhibitors have been identified, des... more In Arabidopsis thaliana, seven cyclin-dependent kinase (CDK) inhibitors have been identified, designated interactors of CDKs or Kip-related proteins (KRPs). Here, the function of KRP6 was investigated during cell cycle progression in roots infected by plant-parasitic root-knot nematodes. Contrary to expectations, analysis of Meloidogyne incognita-induced galls of KRP6overexpressing lines revealed a role for this particular KRP as an activator of the mitotic cell cycle. In accordance, KRP6overexpressing suspension cultures displayed accelerated entry into mitosis, but delayed mitotic progression. Likewise, phenotypic analysis of cultured cells and nematode-induced giant cells revealed a failure in mitotic exit, with the appearance of multinucleated cells as a consequence. Strong KRP6 expression upon nematode infection and the phenotypic resemblance between KRP6 overexpression cell cultures and root-knot morphology point toward the involvement of KRP6 in the multinucleate and acytokinetic state of giant cells. Along these lines, the parasite might have evolved to manipulate plant KRP6 transcription to the benefit of gall establishment.

Post-transcriptional control of GRF transcription factors by microRNA miR396 and GIF co-activator affects leaf size and longevity

Plant J, 2014

The growth-regulating factors (GRFs) are plant-specific transcription factors. They form complexe... more The growth-regulating factors (GRFs) are plant-specific transcription factors. They form complexes with GRF-interacting factors (GIFs), a small family of transcriptional co-activators. In Arabidopsis thaliana, seven out of the nine GRFs are controlled by microRNA miR396. Analysis of Arabidopsis plants carrying a GRF3 allele insensitive to miR396 revealed a strong boost in the number of cells in leaves, which was further enhanced synergistically by an additional increase of GIF1 levels. Genetic experiments revealed that GRF3 can still increase cell number in gif1 mutants, albeit to a much lesser extent. Genome-wide transcript profiling indicated that the simultaneous increase of GRF3 and GIF1 levels causes additional effects in gene expression compared to either of the transgenes alone. We observed that GIF1 interacts in vivo with GRF3, as well as with chromatin-remodeling complexes, providing a mechanistic explanation for the synergistic activities of a GRF3-GIF1 complex. Interestingly, we found that, in addition to the leaf size, the GRF system also affects the organ longevity. Genetic and molecular analysis revealed that the functions of GRFs in leaf growth and senescence can be uncoupled, demonstrating that the miR396-GRF-GIF network impinges on different stages of leaf development. Our results integrate the post-transcriptional control of the GRF transcription factors with the progression of leaf development.

Arabidopsis SNAREs SYP61 and SYP121 coordinate the trafficking of plasma membrane aquaporin PIP2;7 to modulate the cell membrane water permeability

Plant plasma membrane intrinsic proteins (PIPs) are aquaporins that facilitate the passive moveme... more Plant plasma membrane intrinsic proteins (PIPs) are aquaporins that facilitate the passive movement of water and small neutral solutes through biological membranes. Here, we report that post-Golgi trafficking of PIP2;7 in Arabidopsis thaliana involves specific interactions with two syntaxin proteins, namely, the Qc-SNARE SYP61 and the Qa-SNARE SYP121, that the proper delivery of PIP2;7 to the plasma membrane depends on the activity of the two SNAREs, and that the SNAREs colocalize and physically interact. These findings are indicative of an important role for SYP61 and SYP121, possibly forming a SNARE complex. Our data support a model in which direct interactions between specific SNARE proteins and PIP aquaporins modulate their post-Golgi trafficking and thus contribute to the fine-tuning of the water permeability of the plasma membrane.

Regulation of Cell Division in Arabidopsis

by Dirk Inze and Orit Shaul

Critical Reviews in Plant Sciences, 1996

The study of cell cycle control in plants is expected to contribute to the understanding of plant... more The study of cell cycle control in plants is expected to contribute to the understanding of plants&amp;amp;#39; unique developmental features. The principal regulators of the eukaryotic cell cycle, namely, cyclin-dependent kinases (CDKs) and cyclins, are also conserved in plants. This review is concerned with our present knowledge on cell cycle regulation in Arabidopsis thaliana, which is widely accepted as a

Cloning and characterization of a novel Mg2+/H+ exchanger

by Dirk Inze, Orit Shaul, Gad Galili, and Janice Engler

The EMBO Journal, 1999

Cellular functions require adequate homeostasis of several divalent metal cations, including Mg2+... more Cellular functions require adequate homeostasis of several divalent metal cations, including Mg2+ and Zn2+. Mg2+, the most abundant free divalent cytoplasmic cation, is essential for many enzymatic reactions, while Zn2+ is a structural constituent of various enzymes. Multicellular organisms have to balance not only the intake of Mg2+ and Zn2+, but also the distribution of these ions to various organs. To date, genes encoding Mg2+ transport proteins have not been cloned from any multicellular organism. We report here the cloning and characterization of an Arabidopsis thaliana transporter, designated AtMHX, which is localized in the vacuolar membrane and functions as an electrogenic exchanger of protons with Mg2+ and Zn2+ ions. Functional homologs of AtMHX have not been cloned from any organism. Ectopic overexpression of AtMHX in transgenic tobacco plants render them sensitive to growth on media containing elevated levels of Mg2+ or Zn2+, but does not affect the total amounts of these minerals in shoots of the transgenic plants, AtMHX mRNA is mainly found at the vascular cylinder, and a large proportion of the mRNA is localized in close association with the xylem tracheary elements. This localization suggests that AtMHX may control the partitioning of Mg2+ and Zn2+ between the various plant organs.

Cell Cycle Control in Arabidopsis

by Dirk Inze and Orit Shaul

Although the basic mechanism of cell cycle control is conserved among eukaryotes, its regulation ... more Although the basic mechanism of cell cycle control is conserved among eukaryotes, its regulation differs in each type of organism. Plants have unique developmental features that distinguish them from other eukaryotes. These include the absence of cell migration, the formation of organs throughout the entire life-span from specialized regions called meristems, and the potency of non-dividing cells to re-enter the cell cycle. The study of plant cell cycle control genes is expected to contribute to the understanding of these unique developmental phenomena. The principal regulators of the eukaryotic cell cycle, the cyclin-dependent kinases (CDKs) and cyclins, are conserved in plants. This review focuses on cell cycle regulation in the plant Arabidopsis thaliana. While expression of one Arabidopsis CDK gene, Cdc2aAt, was positively correlated with the competence of cells to divide, expression of a mitotic-like cyclin, cyc1At, was almost exclusively confined to dividing cells. The expression of the Arabidopsis δ-type cyclins appears to be an early stage in the response of plant cells to external and internal stimuli.

Levels of endogenous cytokinins, indole-3-acetic acid and abscisic acid during the cell cycle of synchronized tobacco BY-2 cells

by Orit Shaul and Dirk Inze

FEBS Letters, 1996

... FEBS 17337 FEBS Letters 391 (1996) 175180 Levels of endogenous cytokinins, indole3acetic acid... more

Two Arabidopsis Cyclin Promoters Mediate Distinctive Transcriptional Oscillation in Synchronized Tobacco BY2 Cells

by Sylvia Burssens, Vladimir Mironov, Orit Shaul, Dirk Inze, and Marc. Van Montagu

Proceedings of The National Academy of Sciences, 1996

Cyclins are cell cycle regulators whose proteins oscillate dramatically during the cell cycle. Cy... more Cyclins are cell cycle regulators whose proteins oscillate dramatically during the cell cycle. Cyclin steady-state mRNA levels also fluctuate, and there are indications that both their rate of transcription and mRNA stability are under cell cycle control. Here, we demonstrate the transcriptional regulation of higher eukaryote cyclins throughout the whole cell cycle with a high temporal resolution. The promoters of

A comprehensive analysis of hydrogen peroxide-induced gene expression in tobacco

by Luit Slooten, Dirk Inze, and Frank Breusegem

Proceedings of The National Academy of Sciences, 2003

Hydrogen peroxide plays a central role in launching the defense response during stress in plants.... more Hydrogen peroxide plays a central role in launching the defense response during stress in plants. To establish a molecular profile provoked by a sustained increase in hydrogen peroxide levels, catalase-deficient tobacco plants (CAT1AS) were exposed to high light (HL) intensities over a detailed time course. The expression kinetics of >14,000 genes were monitored by using transcript profiling technology based on cDNA-amplified fragment length polymorphism. Clustering and sequence analysis of 713 differentially expressed transcript fragments revealed a transcriptional response that mimicked that reported during both biotic and abiotic stresses, including the up-regulation of genes involved in the hypersensitive response, vesicular transport, posttranscriptional processes, biosynthesis of ethylene and jasmonic acid, proteolysis, mitochondrial metabolism, and cell death, and was accompanied by a very rapid up-regulation of several signal transduction components. Expression profiling corroborated by functional experiments showed that HL induced photoinhibition in CAT1AS plants and that a short-term HL exposure of CAT1AS plants triggered an increased tolerance against a subsequent severe oxidative stress.

Metabolic engineering of plant cell cultures - towards the new resources of alkaloids

Planta Medica Vol.72 Nr.11, 1031 54th Annual Congress on Medicinal Plant Research. Helsinki, Finl... more

Analysis of the spatial expression pattern of seven Kip related proteins (KRPs) in the shoot apex of Arabidopsis thaliana

Annals of Botany

Kip-related-proteins (KRPs), negative regulators of cell division, have recently been discovered ... more Kip-related-proteins (KRPs), negative regulators of cell division, have recently been discovered in plants but their in planta function is as yet unclear. In this study the spatial expression of all seven KRP genes in shoot apices of Arabidopsis thaliana were compared. In situ hybridization analyses were performed on longitudinal sections of shoot apices from 2-month-old Arabidopsis plants. The study provides evidence for different expression pattern groups. KRP1 and KRP2 expression is restricted to the endoreduplicating tissues. In contrast, KRP4 and KRP5 expression is mainly restricted to mitotically dividing cells. KRP3, KRP6 and KRP7 can be found in both mitotically dividing and endoreduplicating cells. The results suggest differential roles for the distinct KRPs. KRP1 and KRP2 might specifically be involved in the establishment of polyploidy. In contrast, KRP4 and KRP5 might be involved in regulating the progression through the mitotic cell cycle. KRP3, KRP6 and KRP7 might have...

Systems analysis of the responses to long-term magnesium deficiency and restoration in Arabidopsis thaliana

New Phytologist

*Unravelling mechanisms that control plant growth as a function of nutrient availability presents... more *Unravelling mechanisms that control plant growth as a function of nutrient availability presents a major challenge in plant biology. This study reports the first transcriptome response to long-term (1 wk) magnesium (Mg) depletion and restoration in Arabidopsis thaliana. *Before the outbreak of visual symptoms, genes responding to Mg starvation and restoration were monitored in the roots and young mature leaves and compared with the Mg fully supplied as control. *After 1 wk Mg starvation in roots and leaves, 114 and 2991 genes were identified to be differentially regulated, respectively, which confirmed the later observation that the shoot development was more affected than the root in Arabidopsis. After 24 h of Mg resupply, restoration was effective for the expression of half of the genes altered. We emphasized differences in the expression amplitude of genes associated with the circadian clock predominantly in leaves, a higher expression of genes in the ethylene biosynthetic pathw...

Low magnesium status in plants enhances tolerance to cadmium exposure

New Phytologist

In a transcriptomic study of magnesium (Mg) starvation in Arabidopsis, we identified several gene... more In a transcriptomic study of magnesium (Mg) starvation in Arabidopsis, we identified several genes that were differentially regulated which are involved in the detoxification process of nonessential heavy metals such as cadmium (Cd). We further tested the impact of low Mg status on Cd sensitivity in plants. Interestingly, a -Mg pretreatment of 7 d alleviated the bleaching of young leaves caused by Cd. No or little difference in Cd tissue concentration between the +Mg and -Mg plants was observed, suggesting that lower Cd toxicity was probably not attributable to modified root to shoot translocation. Mg deficiency also promoted an increase in the iron (Fe) concentration (up to one-fourth) in Cd-treated leaves. Because high Fe concentrations have previously been reported to prevent the harmful effects of Cd, we explored whether Fe homeostasis plays a role in the Mg-Cd interaction. A protective effect of -Mg pretreatment was also observed on Fe starvation. However, Fe foliar spray parti...

Early transcriptomic changes induced by magnesium deficiency in Arabidopsis thaliana reveal the alteration of circadian clock gene expression in roots and the triggering of abscisic acid-responsive genes

New Phytologist

*Plant growth and development ultimately depend on environmental variables such as the availabili... more *Plant growth and development ultimately depend on environmental variables such as the availability of essential minerals. Unravelling how nutrients affect gene expression will help to understand how they regulate plant growth. *This study reports the early transcriptomic response to magnesium (Mg) deprivation in Arabidopsis. Whole-genome transcriptome was studied in the roots and young mature leaves 4, 8 and 28 h after the removal of Mg from the nutrient solution. *The highest number of regulated genes was first observed in the roots. Contrary to other mineral deficiencies, Mg depletion did not induce a higher expression of annotated genes in Mg uptake. Remarkable responses include the perturbation of the central oscillator of the circadian clock in roots and the triggering of abscisic acid (ABA) signalling, with half of the up-regulated Mg genes in leaves being ABA-responsive. However, no change in ABA content was observed. *The specificity of the response of some Mg-regulated gen...

cell cycle interactome cytoscape file

cell cycle interactome excel file

Expression of a novel-type small proline-rich protein gene of alfalfa is induced by 2,4-dichlorophenoxiacetic acid in dedifferentiated callus cells

Plant molecular biology, 1997

Differential screening of a cDNA library of 2,4-dichlorophenoxiacetic acid (2,4-D)-treated alfalf... more Differential screening of a cDNA library of 2,4-dichlorophenoxiacetic acid (2,4-D)-treated alfalfa (Medicago sativa) callus tissues resulted in the isolation of a 571 bp cDNA clone (MsPRP5) encoding for a proline-rich protein (84 amino acids) with a specific repeat unit of TPVLPPRK/RGRPPPVPP. In addition, a characteristic amino acid block (PPVYK) previously found in other proline-rich proteins also occurs in the C-terminal region of MsPRP5. At the N-terminal, a signal peptide similar to leader sequences of extracellular proteins can be predicted. According to the northern analysis, the corresponding gene is not expressed or is weakly expressed in differentiated vegetative organs and somatic embryos. However the accumulation of MsPRP5 mRNA is auxin concentration-dependent in dedifferentiated callus tissue. An increase in the amount of steady-state mRNA was detected already 20 min after auxin shock (100 microM 2,4-D). Maximum expression was observed at 24-48 h in the presence of 2,4-D...

Changes in hydrogen peroxide homeostasis trigger an active cell death process in tobacco

In transgenic tobacco plants with reduced catalase activity, high levels of hydrogen peroxide (H ... more In transgenic tobacco plants with reduced catalase activity, high levels of hydrogen peroxide (H 2 O 2 ) can accumulate under photorespiratory conditions. Such a perturbation in H 2 O 2 homeostasis induced cell death in clusters of palisade parenchyma cells, primarily along the veins. Ultrastructural alterations, such as chromatin condensation and disruption of mitochondrial integrity, took place before cell death. Furthermore, enhanced transcript levels of mitochondrial defense genes accompanied these mitochondrial changes. Pharmacological data indicated that the initiation and execution of cell death require de novo protein synthesis and that the signal transduction pathway leading to cell death involved changes in ion homeostasis, (de)phosphorylation events and an oxidative burst, as observed during hypersensitive responses. This oxidase-dependent oxidative burst is essential for cell death, but it is not required for the accumulation of defense proteins, suggesting a more prominent role for the oxidative burst in abiotic stress-induced cell death.

Mass spectrometry-based sequencing of lignin oligomers

Plant physiology, 2010

Although the primary structure of proteins, nucleic acids, and carbohydrates can be readily deter... more Although the primary structure of proteins, nucleic acids, and carbohydrates can be readily determined, no sequencing method has been described yet for the second most abundant biopolymer on earth (i.e. lignin). Within secondary-thickened plant cell walls, lignin forms an aromatic mesh arising from the combinatorial radical-radical coupling of monolignols and many other less abundant monomers. This polymerization process leads to a plethora of units and linkage types that affect the physicochemical characteristics of the cell wall. Current methods to analyze the lignin structure focus only on the frequency of the major monomeric units and interunit linkage types but do not provide information on the presence of less abundant unknown units and linkage types, nor on how linkages affect the formation of neighboring linkages. Such information can only be obtained using a sequencing approach. Here, we describe, to our knowledge for the first time, a sequencing strategy for lignin oligome...

The elongata mutants identify a functional Elongator complex in plants with a role in cell proliferation during organ growth

Proceedings of The National Academy of Sciences, 2005

The key enzyme for transcription of protein-encoding genes in eukaryotes is RNA polymerase II (RN... more The key enzyme for transcription of protein-encoding genes in eukaryotes is RNA polymerase II (RNAPII). The recruitment of this enzyme during transcription initiation and its passage along the template during transcription elongation is regulated through the association and dissociation of several complexes. Elongator is a histone acetyl transferase complex, consisting of six subunits (ELP1-ELP6), that copurifies with the elongating RNAPII

The cyclin-dependent kinase inhibitor KRP6 induces mitosis and impairs cytokinesis in giant cells induced by plant-parasitic nematodes in Arabidopsis

In Arabidopsis thaliana, seven cyclin-dependent kinase (CDK) inhibitors have been identified, des... more In Arabidopsis thaliana, seven cyclin-dependent kinase (CDK) inhibitors have been identified, designated interactors of CDKs or Kip-related proteins (KRPs). Here, the function of KRP6 was investigated during cell cycle progression in roots infected by plant-parasitic root-knot nematodes. Contrary to expectations, analysis of Meloidogyne incognita-induced galls of KRP6overexpressing lines revealed a role for this particular KRP as an activator of the mitotic cell cycle. In accordance, KRP6overexpressing suspension cultures displayed accelerated entry into mitosis, but delayed mitotic progression. Likewise, phenotypic analysis of cultured cells and nematode-induced giant cells revealed a failure in mitotic exit, with the appearance of multinucleated cells as a consequence. Strong KRP6 expression upon nematode infection and the phenotypic resemblance between KRP6 overexpression cell cultures and root-knot morphology point toward the involvement of KRP6 in the multinucleate and acytokinetic state of giant cells. Along these lines, the parasite might have evolved to manipulate plant KRP6 transcription to the benefit of gall establishment.

Post-transcriptional control of GRF transcription factors by microRNA miR396 and GIF co-activator affects leaf size and longevity

Plant J, 2014

The growth-regulating factors (GRFs) are plant-specific transcription factors. They form complexe... more The growth-regulating factors (GRFs) are plant-specific transcription factors. They form complexes with GRF-interacting factors (GIFs), a small family of transcriptional co-activators. In Arabidopsis thaliana, seven out of the nine GRFs are controlled by microRNA miR396. Analysis of Arabidopsis plants carrying a GRF3 allele insensitive to miR396 revealed a strong boost in the number of cells in leaves, which was further enhanced synergistically by an additional increase of GIF1 levels. Genetic experiments revealed that GRF3 can still increase cell number in gif1 mutants, albeit to a much lesser extent. Genome-wide transcript profiling indicated that the simultaneous increase of GRF3 and GIF1 levels causes additional effects in gene expression compared to either of the transgenes alone. We observed that GIF1 interacts in vivo with GRF3, as well as with chromatin-remodeling complexes, providing a mechanistic explanation for the synergistic activities of a GRF3-GIF1 complex. Interestingly, we found that, in addition to the leaf size, the GRF system also affects the organ longevity. Genetic and molecular analysis revealed that the functions of GRFs in leaf growth and senescence can be uncoupled, demonstrating that the miR396-GRF-GIF network impinges on different stages of leaf development. Our results integrate the post-transcriptional control of the GRF transcription factors with the progression of leaf development.

Arabidopsis SNAREs SYP61 and SYP121 coordinate the trafficking of plasma membrane aquaporin PIP2;7 to modulate the cell membrane water permeability

Plant plasma membrane intrinsic proteins (PIPs) are aquaporins that facilitate the passive moveme... more Plant plasma membrane intrinsic proteins (PIPs) are aquaporins that facilitate the passive movement of water and small neutral solutes through biological membranes. Here, we report that post-Golgi trafficking of PIP2;7 in Arabidopsis thaliana involves specific interactions with two syntaxin proteins, namely, the Qc-SNARE SYP61 and the Qa-SNARE SYP121, that the proper delivery of PIP2;7 to the plasma membrane depends on the activity of the two SNAREs, and that the SNAREs colocalize and physically interact. These findings are indicative of an important role for SYP61 and SYP121, possibly forming a SNARE complex. Our data support a model in which direct interactions between specific SNARE proteins and PIP aquaporins modulate their post-Golgi trafficking and thus contribute to the fine-tuning of the water permeability of the plasma membrane.