Translational plant biology
Activity description
In the last decade, the metal homeostasis group at InBioS-PhytoSYSTEMS has developed a research program aiming at a better understanding of metal homeostasis mechanisms in photosynthetic organisms, with both functional and evolutionary perspectives, and has been mainly focusing on unicellular algae and Arabidopsis relatives with contrasting metal homeostasis as models. The cornerstone of our research interests is the understanding of the adaptation of organisms to their environment and their response to abiotic stress (i.e. metal deficiency or excess). To examine these questions, the group has developed expertise in plant physiology, genetics, genomics, transcriptomics and bioinformatics.
The following projects are currently running in the lab:
1. Metal homeostasis and tolerance in algae.
We are using the unicellular green alga Chlamydomonas reinhardtii as model to investigate the response to short term and long term metal imbalance.
Cadmium is one of the most toxic substances present in the environment and represents a major threat to ecosystems and human health. We initiated an experimental evolution project aiming at identifying adaptive mechanisms involved in cadmium tolerance in Chlamydomonas. Exposing populations of Chlamydomonas to cadmium during many generations and over large time scales is used to decipher the mechanisms underlying adaptive evolution, the mutation rate in genomes and the cost/benefit on fitness. The evolutionary derived populations are deeply phenotyped (growth rate, chlorophyll content, ionomic profiling, cadmium tolerance tests, respiration and photosynthesis rates and gene expression by RNA-Seq) and genotyped (genome re-sequencing).
More recently, with ULiege colleagues (Drs. Tom Druet and Pierre Cardol), natural variation in Chlamydomonas is exploited to develop a MAGIC (Multiparent Advanced Generation Inter-Cross) experimental design to uncover the genetic architecture of important traits such as photosynthesis, biomass production and nutrient homeostasis.
Funding: F.R.S.-FNRS (MIS) and ULiège (ARC)
People: Sara Esteves, Alice Jadoul, Dr. Cécile Nouet
Collaborators: Dr. Tom Druet (GIGA-R, ULiège), Dr. Pierre Cardol (InBioS, ULiège), Prof. Claire Remacle (InBioS, ULiège), Gwenaëlle Gain (InBioS, ULiège), Fabrizio Iacono (InBioS, ULiège).
Alumni: Dr. Stanislas Thiriet-Rupert
2. Metal hyperaccumulation and hypertolerance in A. halleri
An important research topic in the group currently focuses on the evolution and the mechanisms of metal hyperaccumulation and tolerance in the pseudometallophyte Brassicaceae Arabidopsis halleri. A. halleri, as so called hyperaccumulator, can live on soils heavily polluted by metals and possess the ability to accumulate extraordinarily high concentrations of these metals in above-ground tissues without toxicity symptoms (up to 5.4% Zn and/or 0.3% Cd leaf dry biomass). A combination of genetic, comparative transcriptomic and functional genomic approaches identified candidate genes which are constitutively over-expressed in A. halleri compared to A. thaliana and which may have a role in metal tolerance and/or hyperaccumulation. Overall, metal hyperaccumulation evolved through alterations of metal homeostasis networks in comparison to the non-accumulator model species A. thaliana.
Moreover, within the European populations of A. halleri, the colonization of anthropogenic metal-contaminated sites (metallicolous populations) from nearby non-polluted sites (non-metallicolous populations) is thought to have taken place fairly recently and independently. Hypertolerance and hyperaccumulation properties of metallicolous populations thus potentially evolved using distinct genetic mechanisms. In addition, even though Zn hyperaccumulation, Zn and Cd hypertolerance have been suggested as a species-wide trait in A. halleri, substantial intraspecific variation has been observed among M and NM populations. Identifying the mechanisms underlying this natural variation in topical.
Several A. halleri projects are currently ongoing in the group:
- We pursue the functional characterization of candidate genes for zinc/cadmium hyperaccumulation and hypertolerance, including the biochemical characterization of metal-binding to transporters;
- We investigate the extensive intraspecific variation for Zn hyperaccumulation and hypertolerance observed between metallicolous and non-metallicolous A. halleri populations. Practically, quantitative genetic, whole (epi)genome sequencing and RNA-Seq approaches are combined to examine the mechanisms of local adaptation to metal-polluted soils in A. halleri. The group recently developed A. halleri reference genome and transcriptome, as well as considerable resources allowing the comparison of A. halleri ecotypes;
- Comparing A. thaliana and A. halleri, we aim at identifying mechanisms that allow growth of plants in extreme environments, focusing on mechanisms taking place in the root tip;
- We recently initiated a project to analyze the microbiome in the A. halleri rhizosphere.
Funding: F.R.S.-FNRS (PDR, Asp), FRIA, Belspo
People: Julien Spielmann, Amandine Bertrand, Noémie Thiébaut
Collaborators: Prof. Moreno Galleni (InBioS, ULiège), Prof. Denis Baurain (InBioS, ULiège), Prof. Nathalie Verbruggen (ULB, Belgium), Prof. Ute Krämer (University of Bochum, Germany), Drs. Hélène Frérot, Maxime Pauwels, Vincent Castric and Sylvain Legrand (Université de Lille, France), Prof. Stephan Clemens (University of Bayreuth, Germany) and Dr. F. Gösti (SupAgro-INRA, Montpellier). The group also contributes to an international research network funded by the CNRS, “Groupement de recherche international” (GDRI) LOCOMET, “Transport, localization and complexation of metals in hyperaccumulating plants” coordinated by our collaborators in Lille, France.
Alumni: Dr. Ceasar Antony Stanislaus, Dr. Maxime Scheepers, Dr. Gilles Lekeux
3. Zinc deficiency and Zinc/Iron interactions in Arabidopsis thaliana
Zinc is an essential micronutrient for all organisms. It is required as co-factor for enzymatic activity or as structural constituent of proteins (e.g. Zn-finger transcription factors). In plants, zinc is important for increased resistance against abiotic stress (e.g. salt), resistance against pathogen attack and overall positive plant performance. In contrast, excess zinc is toxic and results in plant chlorosis, stunted growth and root deformations among other symptoms. Proper zinc homeostasis in plants has also major implications for human nutrition. About one third of the human population is estimated to suffer from zinc deficiency. This calls for a better unravelling of zinc metabolic pathways, including sensing and signalling, in plants which are the base of the food pyramid.
In this context, we are using transcriptomics and (phospho)-proteomics to unravel early quantitative changes in gene expression, protein abundance and phosphorylation status induced by sudden changes in Zn availability in Arabidopsis thaliana. Functional characterization of a few selected candidates is ongoing using plant molecular genetics in both Arabidopsis thaliana and Brachypodium dystachion.
Moreover, deficiency or excess of one metal can affect the homeostasis of other metal nutrients, often resulting in metal imbalance, due to competition for uptake or permissive specificity of metal transporters. In this context, we are also using A. thaliana mutants to examine the cross-talks that exists between the zinc and iron homeostasis networks.
Funding: F.R.S.-FNRS (CDR), FRIA, FZ Jülich
People: Sahand Amini, Dr. Cécile Nouet
Collaborators: Prof. Michelle Watt and Dr. Borjana Arsova (Forschungszentrum Jülich, Germany), Prof. Edwin de Pauw (Mass Spectrometry, ULiège).
4. The Ecosol project
Our group is responsible for the scientific coordination of this Research and Innovation project (Ecosol: Attractiveness, greening and valorization of industrial wasteland during pre- and post-sanitation periods) funded by the FEDER (European Fund for Regional Development) and the Walloon Region, and grouping five ULiège teams (analytical chemistry, pharmacognosy, agronomy, pedology) in collaboration with the SPAQuE, a public company specializing in the rehabilitation of industrial wastelands. The project objective is to test the possibility of production of high added-value molecules by plants grown on industrial sites not yet rehabilitated. The site of a former chemical factory, “Produits Chimiques d’Auvelais” (PCA, 5.5 ha) which operated between 1850 and 1980 and located in Wallonia was selected as model study site with multi-metal contamination. In addition to the coordination of the project, we are directly responsible for:
(i) the physiological and genetic characterization of Alliaria petiolata, a brassicaceae found at the PCA site. Combining plant physiology, transcriptomics and population genetics approaches, we are examining the mechanisms of metal tolerance of the species in lab and field experiments and aiming to determine whether its ability to colonize metal-polluted soils rely on adaptation or on phenotypic plasticity.
(ii) field trials at the PCA site, started in fall 2018 to evaluate the performance of different Oilseed rape (Brassica napus) varieties, in a joint effort with our agronomy partner.
This applied project is in direct connection with our interest for adaptation in Brassicaceae.
Funding: EDRF and Wallonia
People: Dr. Cécile Nouet and Emilie Detry
Collaborators: Prof. Edwin de Pauw (Mass Spectrometry, ULiège), Prof. Michel Frederich (CIRM, ULiège), Prof. Gilles Colinet (Gbx Agro Biotech, ULiège), Prof. Bernard Bodson (Gbx Agro Biotech, ULiège).
Former group members:
Dr. Jean-Benoit Charlier, Attaché de direction, Société Wallonne des Eaux, Belgium
Dr. Clémentine Laurent, Project Manager, EyeD Pharma, Belgium
Dr. Sol Schvartzman, Bioinformatics Scientist, Diagenode, Belgium
Dr. Borjana Arsova, Root Dynamics Group, IBG-2 - Plant Sciences, Institut für Bio- und Geowissenschaften (IBG) Forschungszentrum Jülich, Germany
Gwenaëlle Gain, PhD student, Physiology and Genetics of Microalgae, ULiège, Belgium
Dr. Nazeer Fataftha, Postdoc, Umeå plant science center (UPSC), Sweden
Dr. Amandine Vigneron, Scientific et technical coordinator, Anses (Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail), France
Members
Amini Sahand
Cardoso Esteves Sara Marina
Jadoul Alice
Detry Emilie
Nouet Cécile, Dr.
Spielmann Julien
Thiebaut Noémie
Hanikenne Marc, Dr.
Bertrand Amandine (avec Phylogénomique des Eukaryotes)
5 most representative publications
1) M.S. Schvartzman Echenique, M. Corso, N. Fataftha, M. Scheepers, C. Nouet, B. Bosman, M. Carnol, P. Motte, N. Verbruggen, M. Hanikenne (2018). Adaptation to high zinc depends on distinct mechanisms in metallicolous populations of Arabidopsis halleri. New Phytol 218:269-82 (I.F. 2017: 7.433)
http://hdl.handle.net/2268/217633
2) G. Lekeux, C. Laurent, M. Joris, A. Jadoul, D. Jiang, B. Bosman, M. Carnol, P. Motte, Z. Xiao, M. Galleni, M. Hanikenne (2018). di-Cysteine motifs in the C-terminus of plant HMA4 proteins confer nanomolar affinity for zinc and are essential for HMA4 function in vivo. J Exp Bot 69: 5547-60 (I.F.2017: 5.354)
http://hdl.handle.net/2268/230719
3) J.B. Charlier, C. Polese, C. Nouet, M. Carnol, B. Bosman, U. Krämer, P. Motte, M. Hanikenne (2015). Zinc triggers a complex transcriptional and post-transcriptional regulation of the metal homeostasis gene FRD3 in Arabidopsis relatives. J Exp Bot 66: 3865-3878 (I.F. 5.677)
http://hdl.handle.net/2268/181578
4) C. Nouet, J.B. Charlier, M. Carnol, B. Bosman, F. Farnir, P. Motte, M. Hanikenne (2015). Functional analysis of the three HMA4 copies of the metal hyperaccumulator Arabidopsis halleri. J Exp Bot 66: 5783-95 (I.F.: 5.677)
http://hdl.handle.net/2268/181581
5) M. Hanikenne*, J. Kroymann*, A. Trampczynska, M. Bernal, P. Motte, S. Clemens, U. Krämer (2013) Hard Selective Sweep and Ectopic Gene Conversion in a Gene Cluster Affording Environmental Adaptation. PLoS Genet 9:1003707 (I.F.: 8.167)
