References of "Tocquin, Pierre"
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See detailIntegrating roots into a whole plant network of flowering time genes in Arabidopsis thaliana
Bouché, Frédéric ULg; D'Aloia, Maria; Tocquin, Pierre ULg et al

in Scientific Reports (2016), 6

Molecular data concerning the involvement of roots in the genetic pathways regulating floral transition are lacking. In this study, we performed global analyses of the root transcriptome in Arabidopsis in ... [more ▼]

Molecular data concerning the involvement of roots in the genetic pathways regulating floral transition are lacking. In this study, we performed global analyses of the root transcriptome in Arabidopsis in order to identify flowering time genes that are expressed in the roots and genes that are differentially expressed in the roots during the induction of flowering. Data mining of public microarray experiments uncovered that about 200 genes whose mutations are reported to alter flowering time are expressed in the roots (i.e. were detected in more than 50% of the microarrays). However, only a few flowering integrator genes passed the analysis cutoff. Comparison of root transcriptome in short days and during synchronized induction of flowering by a single 22-h long day revealed that 595 genes were differentially expressed. Enrichment analyses of differentially expressed genes in root tissues, gene ontology categories, and cis-regulatory elements converged towards sugar signaling. We concluded that roots are integrated in systemic signaling, whereby carbon supply coordinates growth at the whole plant level during the induction of flowering. This coordination could involve the root circadian clock and cytokinin biosynthesis as a feed forward loop towards the shoot. [less ▲]

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See detailFunctional analysis of PEBP genes in root chicory (Cichorium intybus)
Saintmard, Nicolas ULg; Tocquin, Pierre ULg; Périlleux, Claire ULg

Poster (2016, June 09)

Manipulating plant architecture is key to increase crop yield. In this perspective, basic knowledge on the molecular mechanisms regulating plant growth and development will be fundamental for the future ... [more ▼]

Manipulating plant architecture is key to increase crop yield. In this perspective, basic knowledge on the molecular mechanisms regulating plant growth and development will be fundamental for the future of agriculture. Recent progress indicates that a family of plant genes, homologous to POSPHADITYLETHANOLAMINE-BINDING PROTEINS (PEBP) in other eukaryotes, plays critical roles in controlling shoot development traits such as branching, flowering, bud dormancy or tuberization. Very little is known however on the functions of these genes in root development. The current research will attempt to answer this question in the case of Cichorium intybus, a biannual plant cultivated for the extraction of inulin (a polymer of fructose) from its root. Functional analyses will include expression kinetics, complementation tests in Arabidopsis mutants and creation of PEBP- overexpressing or silencing chicory plants. The preliminary steps of the project are the identification of PEBP genes in chicory by in silico analyses, the determination of the time of the storage root initiation and the establishment of a regeneration protocol for the genetic transformation. [less ▲]

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See detailThe chlorophyll a fluorescence induction curve in the green microalga Haematococcus pluvialis: Further insight into the nature of the P-S-M fluctuation and its relationship with the "low-wave" phenomenon at steady-state
Fratamico, Anthony ULg; Tocquin, Pierre ULg; Franck, Fabrice ULg

in Photosynthesis Research (2016), 128(3), 271-285

Chlorophyll fluorescence is an information-rich signal which provides an access to the management of light absorbed by PSII. A good example of this is the succession of fast fluorescence fluctuations ... [more ▼]

Chlorophyll fluorescence is an information-rich signal which provides an access to the management of light absorbed by PSII. A good example of this is the succession of fast fluorescence fluctuations during light-induced photosynthetic induction after dark-adaptation. During this period, the fluorescence trace exhibits several inflexion points: O-J-I-P-S-M-T. Thereas the OJIP part of this kinetics has been the subject of many studies, the processes that underly the PSMT transient are less understood. Here, we report an analysis of the PSMT phase in the green microalga Haematococcus pluvialis in terms of electron acceptors and light use by photochemistry, fluorescence and non-photochemical quenching (NPQ). We identify additional sub-phases between P and S delimited by an inflexion point, that we name Q, found in the second time-scale. The P-Q phase expresses a transient photochemical quenching specifically due to alternative electron transport to oxygen. During the transition from Q to S, the NPQ increases and then relaxes during the S-M phase in about 1 min. It is suggested that this transient NPQ observed during induction is a high energy state quenching (qE) dependent the alternative electron transport to molecular oxygen. We further show that this NPQ is of the same nature than the NPQ, known as the low-wave phenomenon, which is transiently observed after a saturating light pulse given at steady-state. In both cases, the NPQ is oxygen-dependent. This NPQ is observed at external pH 6.0, but not at pH 7.5, which seems correlated with faster saturation of the PQ pool at pH 6.0. [less ▲]

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See detailRhizosecreted proteases inhibition for the improvement of recombinant protein production in Arabidopsis thaliana
Lallemand, Jérôme ULg; Périlleux, Claire ULg; Tocquin, Pierre ULg

Poster (2016, April)

Plant-based biopharmaceuticals have gained a lot of interest in the past decade due to their reduced cost and relative safety compared to mammalian cell cultures. While the first plant-made recombinant ... [more ▼]

Plant-based biopharmaceuticals have gained a lot of interest in the past decade due to their reduced cost and relative safety compared to mammalian cell cultures. While the first plant-made recombinant proteins are now reaching the market, the production systems still need improvements to maximize their competitiveness. Optimizing production hosts requires the identification and subsequent inhibition of the most active endogenous peptidases, proteolysis being one of the main factors limiting yields. The aim of our study was to identify root-secreted proteases of Arabidopsis thaliana involved in target protein degradation (BSA) and inhibit them in vivo. Biochemical analyses identified serine proteases as the main class responsible for BSA degradation. An RT-qPCR experiment led to the choice of the serine protease gene SBT4.12 and its homologs as targets for an amiRNA-mediated silencing approach. Arabidopsis amiRNA-expressing lines showed lower levels of expression for SBT4.12 and reduced proteolytic activity in their rhizosecreted extracts. Crossing these lines with recombinant protein producing lines could lead to an improved production platform for proteins of interest. [less ▲]

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See detailFLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana
Bouché, Frédéric ULg; Lobet, Guillaume ULg; Tocquin, Pierre ULg et al

in Nucleic Acids Research (2016), 44(Database), 11671171

Flowering is a hot topic in Plant Biology and important progress has been made in Arabidopsis thaliana toward unravelling the genetic networks involved. The increasing complexity and the explosion of ... [more ▼]

Flowering is a hot topic in Plant Biology and important progress has been made in Arabidopsis thaliana toward unravelling the genetic networks involved. The increasing complexity and the explosion of literature however require development of new tools for information management and update. We therefore created an evolutive and interactive database of flowering time genes, named FLOR-ID (Flowering-Interactive Database), that is available freely at http://www.flor-id.org. The hand-curated database contains information on 306 genes and links to 1595 publications gathering the work of more than 4500 authors. Gene function and interactions within the flowering pathways were inferred from the analysis of related publications, included in the database and translated into interactive manually drawn snapshots. [less ▲]

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See detailModeling inflorescence development in tomato
Périlleux, Claire ULg; Lobet, Guillaume ULg; Tocquin, Pierre ULg

Conference (2015, June)

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See detailExtracellular peptidase hunting for improvement of protein production in plant cells and roots
Lallemand, Jérôme ULg; Bouché, Frédéric ULg; Desiron, Carole et al

Poster (2015, June)

Plant-based biopharmaceuticals have gained a lot of interest in the past decade due to their reduced cost and relative safety compared to mammalian cell cultures. While the first plant-made recombinant ... [more ▼]

Plant-based biopharmaceuticals have gained a lot of interest in the past decade due to their reduced cost and relative safety compared to mammalian cell cultures. While the first plant-made recombinant proteins are now reaching the market, the production systems still need improvements to maximize their competitiveness, proteolysis being one of the main factors limiting the yields. Identifying and inhibiting in vivo endogenous proteases involved in the degradation of recombinant proteins could then lead to a significant increase in production yields. In this study, we focused on two different production systems in Arabidopsis thaliana: rhizosecretion and cell suspensions. Extracellular proteases of both systems were used in vitro to study the conditions of target protein degradation (Bovine Serum Albumine, BSA). First, proteases from both systems degrade BSA at both acidic and neutral-to-basic pH conditions. Then, serine and metallopeptidases were shown to be the main protease classes responsible for BSA degradation by rhizosecreted proteomes or extracellular cell culture media, respectively. Finally, the biochemical tests were coupled to a bioinformatics analysis of publicly available transcriptomic data, in order to reduce the number of the proteases most likely involved in BSA degradation. Using this method, only five serine proteases and two metallopeptidases remain candidates for an amiRNA-mediated in vivo inhibition. [less ▲]

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See detailGenetic Control of Flowering Time in Arabidopsis: an Interactive Database
Bouché, Frédéric ULg; Lobet, Guillaume ULg; Tocquin, Pierre ULg et al

Poster (2015, March 12)

The transition to flowering is an essential step of the plant life cycle that is tightly controlled by both endogenous and environmental cues. Its regulation is extremely complex and involves hundreds of ... [more ▼]

The transition to flowering is an essential step of the plant life cycle that is tightly controlled by both endogenous and environmental cues. Its regulation is extremely complex and involves hundreds of genes that are part of highly interconnected pathways. Our knowledge of the molecular mechanisms governing the floral induction of Arabidopsis thaliana increases quickly and a significant number of reviews are published every year on this topic. However, most of them focus on a single pathway without highlighting the interconnections existing between them. Furthermore, those reviews become rapidly outdated, since our comprehension of the genetic control of flowering time evolves continuously. Hence, we believe that the current landscape of flowering time research in Arabidopsis misses an exhaustive repository of the genes involved in the control of flowering and their regulatory pathways. Here, we present a new interactive resource built around a curated database of the flowering time genes that brings together multiple pieces of information such as their function, the flowering time phenotype of mutants and overexpressing lines, the related key publications, etc. Our website thus gives access to a curated and exhaustive list of the genes involved in the regulation of flowering time in Arabidopsis as well as the regulatory pathways controlling their expression. Because of its flexibility, the database is highly dynamic and will be periodically updated with the future breakthroughs in this domain. [less ▲]

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See detail“Rhizoponics”: a novel hydroponic rhizotron for root system analyses on mature Arabidopsis thaliana plants
Mathieu, Laura ULg; Lobet, Guillaume ULg; Tocquin, Pierre ULg et al

Poster (2015, March 10)

Well-developed and functional roots are critical to support plant life and reach high crop yields. Their study however, is hampered by their underground growth and characterizing complex root system ... [more ▼]

Well-developed and functional roots are critical to support plant life and reach high crop yields. Their study however, is hampered by their underground growth and characterizing complex root system architecture therefore remains a challenge. In the model plant Arabidopsis thaliana, in vitro culture remains the easiest and preferred method to study root development, which limits the analyses to young seedlings. We present here an innovative design of hydroponic rhizotron (rhizoponics) designed for the root system analysis of adult plants of Arabidopsis thaliana. [less ▲]

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See detail“Rhizoponics”: a novel hydroponic rhizotron for root system analyses on mature Arabidopsis thaliana plants
Mathieu, Laura ULg; Lobet, Guillaume ULg; Tocquin, Pierre ULg et al

in Plant Methods (2015), 11

We present here an innovative design of hydroponic rhizotrons (rhizoponics) adapted to Arabidopsis thaliana. The setup allows to simultaneously characterize the RSA and shoot development from seedling to ... [more ▼]

We present here an innovative design of hydroponic rhizotrons (rhizoponics) adapted to Arabidopsis thaliana. The setup allows to simultaneously characterize the RSA and shoot development from seedling to adult stages, i.e. from seed to seed. This system offers the advantages of hydroponics such as control of root environment and easy access to the roots for measurements or sampling. Being completely movable and low cost, it can be used in controlled cabinets. We chose the case of cadmium treatment to illustrate potential applications, from cell to organ levels. [less ▲]

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See detailExtracellular peptidase hunting for improvement of protein production in plant cells and roots
Lallemand, Jérôme ULg; Bouché, Frédéric ULg; Desiron, Carole et al

in Frontiers in Plant Science (2015), 6(37),

Plant-based recombinant protein production systems have gained an extensive interest over the past few years, because of their reduced cost and relative safety. Although the first products are now ... [more ▼]

Plant-based recombinant protein production systems have gained an extensive interest over the past few years, because of their reduced cost and relative safety. Although the first products are now reaching the market, progress are still needed to improve plant hosts and strategies for biopharming. Targeting recombinant proteins toward the extracellular space offers several advantages in terms of protein folding and purification, but degradation events are observed, due to endogenous peptidases. This paper focuses on the analysis of extracellular proteolytic activities in two production systems: cell cultures and root-secretion (rhizosecretion), in Arabidopsis thaliana and Nicotiana tabacum. Proteolytic activities of extracellular proteomes (secretomes) were evaluated in vitro against two substrate proteins: bovine serum albumin (BSA) and human serum immunoglobulins G (hIgGs). Both targets were found to be degraded by the secretomes, BSA being more prone to proteolysis than hIgGs. The analysis of the proteolysis pH-dependence showed that target degradation was mainly dependent upon the production system: rhizosecretomes contained more peptidase activity than extracellular medium of cell suspensions, whereas variations due to plant species were smaller. Using class-specific peptidase inhibitors, serine and metallopeptidases were found to be responsible for degradation of both substrates. An in-depth in silico analysis of genomic and transcriptomic data from Arabidopsis was then performed and led to the identification of a limited number of serine and metallo-peptidases that are consistently expressed in both production systems. These peptidases should be prime candidates for further improvement of plant hosts by targeted silencing. [less ▲]

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See detailOn the necessity and biological significance of threshold-free regulon prediction outputs
Rigali, Sébastien ULg; Nivelle, Renaud; Tocquin, Pierre ULg

in Molecular Biosystems (2015), 11

The in silico prediction of cis-acting elements in a genome is an efficient way to quickly obtain an overview of the biological processes controlled by a trans-acting factor, and connections between ... [more ▼]

The in silico prediction of cis-acting elements in a genome is an efficient way to quickly obtain an overview of the biological processes controlled by a trans-acting factor, and connections between regulatory networks. Several regulon prediction web tools are available, designed to identify DNA motifs predicted to be bound by transcription factors using position weight matrix-based algorithms. In this paper we expose and discuss the conflicting objectives of software creators (bioinformaticians) and software users (biologists), who aim for reliable and exhaustive prediction outputs, respectively. Software makers, concerned with providing tools that minimise the number of false positive hits, often impose a stringent threshold score for a sequence to be included in the list of the putative cis-acting sites. This rigidity eventually results in the identification of strongly reliable but largely straightforward sites, i.e. those associated with genes already anticipated to be targeted by the studied transcription factor. Importantly, this biased identification of strongly bound sequences contrasts with the biological reality where, in many circumstances, a weak DNA-protein interaction is required for the appropriate gene's expression. We show here a series of transcriptionally controlled systems involving weakly bound cis-acting elements that could never have been discovered because of the policy of preventing software users from modifying the screening parameters. Proposing only trustworthy prediction outputs thus prevents biologists from fully utilising their knowledge background and deciding to analyse statistically irrelevant hits that could nonetheless be potentially involved in subtle, unexpected, though essential cis-trans relationships. [less ▲]

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See detailIdentifying root-secreted proteases in Arabidopsis thaliana: an Activity-Based Protein Profiling approach.
Lallemand, Jérôme ULg; Périlleux, Claire ULg; Tocquin, Pierre ULg

Poster (2014, May 15)

Proteases are involved in many physiological processes during the whole life of the plant, such as embryonic development, defense against pathogens, nutrition or mycorrhiza creation. However, the ... [more ▼]

Proteases are involved in many physiological processes during the whole life of the plant, such as embryonic development, defense against pathogens, nutrition or mycorrhiza creation. However, the functions of many of the 800 proteases of Arabidopsis thaliana still remain unknown. Besides discovering new functions, studying proteases can also result in improving plant biotechnology. Indeed, plants can be used as hosts for recombinant protein production. Some proteins of interest require to be secreted in order to fold properly, but production yields are limited due to their degradation by endogenous extracellular proteases. The aim of our study is to identify active root-secreted proteases of Arabidopsis thaliana. Their activity was first analyzed by in vitro incubation with a target protein (BSA) at different values of pH and in the presence of proteases inhibitors. This analysis identified serine proteases as the major protease class involved in BSA degradation. Then, an Activity-Based Protein Profiling approach led to the labeling of two active serine proteases in the root-secreted sample. Finally, a further step towards the identification by mass spectrometry, based on affinity purification, was developed. [less ▲]

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See detailFlowering Goes Underground
Bouché, Frédéric ULg; Lobet, Guillaume ULg; D'Aloia, Maria ULg et al

Conference (2014, May 15)

Flowering is a crucial step in plant life cycle and is therefore tightly controlled by both environmental and endogenous cues. The involvement of the aerial organs of the plant in the molecular mechanisms ... [more ▼]

Flowering is a crucial step in plant life cycle and is therefore tightly controlled by both environmental and endogenous cues. The involvement of the aerial organs of the plant in the molecular mechanisms controlling floral transition has been extensively documented while the participation of the roots remains poorly investigated. However, the induction of flowering by photoperiod involves systemic signals that move in the phloem from leaves to sinks, and hence presumably reach the roots. We therefore performed a transcriptomic analysis of the roots during the induction of flowering in Arabidopsis thaliana and indeed identified a large number of differentially expressed genes. A reverse genetic approach further confirmed the pleiotropic effects of flowering time genes on root architecture. [less ▲]

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See detailStudy of an undershoot in chlorophyll fluorescence signal after a saturating pulse in PAM measurements
Fratamico, Anthony ULg; Cardol, Pierre ULg; Tocquin, Pierre ULg et al

Conference (2014, April 14)

In 1989, Larcher and Neuner have reported the observation of a sudden reversible drop in modulated chlorophyll fluorescence measurements (PAM) immediately after a saturating pulse, and called it “low ... [more ▼]

In 1989, Larcher and Neuner have reported the observation of a sudden reversible drop in modulated chlorophyll fluorescence measurements (PAM) immediately after a saturating pulse, and called it “low-wave”. 25 years later, whereas some papers reported this phenomenon as a trivial detail, scarcely two works have investigated the origin of this particular signal, in which a link with a low CO2 availability seems clear. Our work on Haematococcus pluvialis, a freshwater green microalga, provides a new point of view on this fluorescence undershoot, caused by a rapidly established non-photochemical quenching. We have demonstrated that in the light-adapted state, a low-wave after a saturating flash can be considered as a consequence of an induction process engaged in response to the brief light increase under low CO2 conditions. The non-photochemical quenching during low-waves was found to be dependent on electron transport to oxygen during the preceding flash. Moreover, in conditions in which low-waves were observed in the light-adapted state, the fluorescence induction kinetics in the first minute of lighting after dark-adaptation presented also a reversible strong drop. Nevertheless, at the stationary state, oxygen production and photochemical yield of photosystem II were not affected. Providing a better understanding of the processes underlying low-waves, our work also draws attention on the effect of CO2 concentration on the onset of photosynthesis. [less ▲]

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See detailInflorescence development in tomato: gene functions within a zigzag model.
Périlleux, Claire ULg; Lobet, Guillaume ULg; Tocquin, Pierre ULg

in Frontiers in Plant Science (2014), 5

Tomato is a major crop plant and several mutants have been selected for breeding but also for isolating important genes that regulate flowering and sympodial growth. Besides, current research in ... [more ▼]

Tomato is a major crop plant and several mutants have been selected for breeding but also for isolating important genes that regulate flowering and sympodial growth. Besides, current research in developmental biology aims at revealing mechanisms that account for diversity in inflorescence architectures. We therefore found timely to review the current knowledge of the genetic control of flowering in tomato and to integrate the emerging network into modeling attempts. We developped a kinetic model of the tomato inflorescence development where each meristem was represented by its ‘vegetativeness’ (V), reflecting its maturation state towards flower initiation. The model followed simple rules: maturation proceeded continuously at the same rate in every meristem (dV); floral transition and floral commitment occurred at threshold levels of V; lateral meristems were initiated with a gain of V (ΔV) relative to the V level of the meristem from which they derived. This last rule created a link between successive meristems and gave to the model its zigzag shape. We next exploited the model to explore the diversity of morphotypes that could be generated by varying dV and ΔV and matched them with existing mutant phenotypes. This approach, focused on the development of the primary inflorescence, allowed us to elaborate on the genetic regulation of the kinetic model of inflorescence development. We propose that the lateral inflorescence meristem fate in tomato is closer to an immature flower meristem than to the inflorescence meristem of Arabidopsis. In the last part of our paper, we extend our thought to spatial regulators that should be integrated in a next step for unraveling the relationships between the different meristems that participate to sympodial growth. [less ▲]

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See detailThe hidden half of flowering
Bouché, Frédéric ULg; Mistiaen, Kevin ULg; D'Aloia, Maria ULg et al

Poster (2013, June)

Flowering is one of the most important developmental steps in plant life cycle and is therefore tightly controlled by environmental cues. The involvement of the aerial part of the plant in the molecular ... [more ▼]

Flowering is one of the most important developmental steps in plant life cycle and is therefore tightly controlled by environmental cues. The involvement of the aerial part of the plant in the molecular mechanisms leading to floral transition is well documented while participation of the roots received less attention. Nevertheless, the induction of flowering by photoperiod is known to involve systemic signals that move in phloem sap towards sinks, throughout the plants, including the roots. Transcriptomic analysis of roots tissues during the floral induction of flowering by a single long day of in Arabidopsis thaliana by a single long day allowed us to identify a large number of differentially expressed genes. How mutations We subsequently selected in some candidate genes affect plant development - including root architecture and flowering time - is being to analyze their flowering timefurther analyzed. Further analysis of those genes will permit us to unravel their role in the flowering induction process. [less ▲]

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