To elucidate the cellular signaling pathways linking stress and development of plants
Plant development is remarkably flexible. While each plant has a basic body plan, its exact shape can be adjusted to specific conditions that the plant experiences. How plant root development and growth is influenced by environmental signals is a major question in plant biology. We approach this subject from different angles, ranging from biophysics of protein-lipid interactions, via cellular organization, to worldwide natural variation in plant stress responses. In particular, we focus on the effects of salinity and drought, and more recently also nutrient starvation, on root system architecture.
On of the major aims of the group is to elucidate the molecular and cellular roles of phospholipid-mediated regulation of vesicular trafficking in coordinating root growth and development. Recently, we have discovered that salinity-induced formation of the lipid second messenger phosphatidic acid (PA) affects clathrin-coated vesicle formation and cell polarity, and is required for modulation of root growth in response to salinity. Currently, novel tools are being developed to manipulate localization and activity of phospholipid-metabolizing enzymes, to assess the effect of membrane phospholipid composition on in vivo cellular organization. Another goal will be to uncover the molecular basis of modulation of clathrin-mediated endocytosis and establishment of cell polarity by phospholipids. Finally, we aim to integrate the molecular and cellular data obtained on membrane lipid composition, vesicle transport and polar distribution of protein complexes, to elucidate how these processes coordinate environmental stress and developmental processes on the whole-plant-level.
A parallel line of research focuses on the same biological research question, but uses a genomics approach, rather than a cell biological one, to identify novel loci that contribute to adaptation to salt tolerance. The rationale behind this work is to link the phenotype of a collection of Arabidopsis accessions adapted to specific environmental conditions worldwide, to their genotypes (250K SNP data), using genome-wide association studies (GWAS). In this way, novel loci essential for adaptation to specific conditions, including salinity and nutrient starvation, can be identified. A large phenotypic screen for root system architecture under salinity stress was performed on the Arabidopsis HapMap population. GWAS of these data successfully revealed several promising candidate loci that significantly associate with the capacity of roots to adapt their architecture to stress. Currently, these loci are being followed up by molecular and physiological approaches. Unravelling of the molecular and cellular function of the proteins encoded for by the identified loci (including ion transport, hormone signalling) will be a major goal for the coming years.
Finally, the relevance of root plasticity under salt (and nutrient) stress for plant survival and yield is another question that is addressed. One of the major fundamental research questions in this field is to identify the sodium sensing mechanism of plant roots. Sub-questions to answer are:
-How does the halotropic response (root bending away from salt) contribute to plant yield and survival?
-What is a good root system architecture response of plants to salinity in terms of shoot growth (yield) and plant survival?
Approaches will include the use of tomato, rice and Arabidopsis plants, including mutants, to elucidate the importance of RSA changes and halotropism in stress tolerance. In Arabidopsis, expression of genes controlling auxin transport, ABA synthesis or other genes affecting RSA is specifically manipulated in the root, by using tissue-specific promoters driving amiRNA or OE constructs. This approach should reveal the importance of RSA plasticity for above-ground growth and yield.
Phosphatidic acid (PA) has recently been identified as a lipid second messenger in eukaryotes. In plants, it is typically produced upon several biotic and abiotic stimuli and functions as a docking site for proteins. Using a proteomics approach involving purification on PA-beads followed by mass spectrometry, we identified a set of proteins that have affinity for PA.
Several of these were protein kinases and phosphatases, implicated in various plant physiological responses. At the moment, we are investigating one of these targets, a Snf-1 related protein kinase (SnRK2), which is activated upon exposure of the plant to osmotic stress.
We study the role of PA and its targets in the response of plants to osmotic stress. PA-binding protein kinases and phosphatases implicated in these responses are further characterized with the aim to elucidate the mode of action of PA in affecting protein function and to understand how PA regulation of proteins affects downstream responses.
A differential proteomics screen has been set up to isolate PA-binding candidate proteins that are targeted to the membrane in response to a PA increase. For this purpose, we isolate peripheral membrane proteins of control cells vs. salt-stimulated cells and select PA-binding proteins that are only present in the stimulated sample. In this way, a novel set of PA targets has been identified by mass spectrometry.
We have analyzed the PA-binding sites of the Arabidopsis protein kinases CTR1, SnRK2 and PDK1. Elucidation of the molecular basis of PA-binding will allow us to manipulate PA-binding ability of these and other protein kinases. As such, it will help us establish the function of PA-binding in downstream responses of plants to stress.
There are always possibilities for students to do an internship in our group.
Please enquire for specific projects currently available.
Depending on the length of the practical training period (minimum 4 months), the student can work on several different subprojects, focussed on understanding salt tolerance of plants, hormonal regulation, protein-lipid interactions and/or ecogenomics of root architecture. Each of the projects will involve a diverse array of techniques, including: protein expression and purification, protein kinase assays, lipid binding assays, confocal microscopy, plant physiological assays using mutants and naturally adapted accessions of Arabidopsis, Q-RT-PCR, cloning and plant transformation.
As of March 1, 2016, we have started a new group - Plant Cell Biology - within SILS.
Science Park 904
1098 XH Amsterdam
PhD students: Dorota Kawa, Ruud Korver, Deji Deolu-Ajayi, Iko Koevoets
Technician: Jessica Meyer
Post-docs: Steven Arisz, Yanxia Zhang
I’ve started my PhD in September 2012. My main interest is how plants can change the shape of their Root System Architecture (RSA) in different environments. The main focus of our group is on salt stress, but in my research I extend that question to phosphate starvation. One of the adaptive strategies to survive salinity and other osmotic stresses is to modulate RSA through Main Root growth arrest and decrease of Lateral Root number and length. In low phosphate conditions Main Root growth is arrested, but the number of Lateral Roots usually increases. Saline soils very often have low levels of phosphate, which is one of the major nutrients for plants. This means that at the same time plants have to respond to two different stresses that are shaping their roots in a different manner. I’m interested in the combined effect of salinity and phosphate starvation and how do plants integrate multiple stresses. To answer these questions we use natural variation existing in Arabidopsis. I’m constantly amazed by the fact that so many types of Root System Architecture can be found within one species as well as by the level of root plasticity. With the Genome Wide Association Mapping (GWAS) we mapped couple of novel loci putatively responsible for the developmental adaptations to salt, phosphate starvation and their combined effect. When I’m taking a break from roots, I switch to be biochemist. In my second project I’m characterizing two proteins with already known role in RSA modulation by salt, protein kinases SnRK 2.4 and SnRK 2.10. I search for their down- and upstream interactors, to fill in the gaps in SnRK2.4/2.10 signaling pathway.
Before my technician position in the Plant Cell Biology group of Christa Testerink, I worked on two projects for my Bsc. In one study project, a biochemistry project, I did some research to find a potential Biomarker for the diagnosis of Alzheimer’s disease. For my thesis project, a molecular biology project, I studied the regulation of the cell cycle in yeast. After these studies I wanted to gain experience in a new topic and techniques. This is how I started in the group of Christa Testerink, working in plant science, which was definitely new for me. My current work mainly involves molecular cell biology, genetics and biochemistry. To make life a bit easier for my colleagues :-), I help out with some cloning work, protein expression, gene expression, genotyping, phenotyping, root system architecture (RSA) and of course some lab management. Basically I do a bit of everything, which I enjoy, because I gain a lot of experience in various techniques and I am always busy.
Mostly our group is interested in how plants adapt to abiotic stresses such as salt or phosphate starvation. By looking at the Root System Architecture (RSA) of Arabidopsis, we aim to understand more about how lateral or main roots develop under abiotic stress conditions. From there we could further investigate the molecular and cellular mechanism in responding to these stress conditions. Besides for the model plant Arabidopsis, we are also interested in understanding how the regulatory mechanism works for crops facing abiotic stress to contribute to crops breeding.
My background definitely piqued my interest in Science but it wasn’t until my Masters (in Biotechnology) that I decided on continuing with a PhD in Plant Science, focusing on Salinity stress.
Plants, like animals cannot cope with high levels of NaCl, and react specifically to get rid of these harmful ions. Plants favourably adapt by growing towards soil with lower concentrations of NaCl (halotropism). My Project focuses on identifying the salt sensing mechanism in plants; basically, understanding how exactly plants sense this stress before responding. My initial focus will be on Arabidopsis, but I will also work with tomato and sorghum in the latter stage of my PhD. I will be using GWAS, QTL mapping and necessary molecular tools to determine the underlying sensing mechanism. Understanding how plants respond to salt stress will definitely contribute to maximizing efforts in producing salt tolerant crops.
I obtained my PhD degree in September 2014. My PhD research was focused on the biosynthesis of the novel phytohormone strigolactone and its signal perception in root parasitic plants. After that I have worked in an applied postdoctoral project on the role of strigolactones in crop enhancement under abiotic stresses. During working this project, I became amazed by the remarkable plasticity of plant roots in their response to various soil environments. I since developed a strong interest and ambition to unravel the molecular mechanism of how plants adapt their root growth to cope with abiotic stresses. Therefore, to further study the underlying molecular mechanisms, I started my postdoc research in Plant Cell Biology of the UvA with Prof. dr. Christa Testerink in August 2016. In the group, I am exploring the salt-specific signalling pathways to regulate plant growth responses and ultimately tolerance to soil salinity.
personal website: http://www.uva.nl/profile/y.zhang3
My PhD research was at the lipid signaling lab of Teun Munnik. Using a unicellular green alga (Chlamydomonas) and a vascular plant (Arabidopsis) as models, I studied the metabolism of signalling lipids, particularly phosphatidic acid, in response to environmental stresses such as cold and salinity (http://dare.uva.nl/record/1/326237).
In 2010 I joined Christa Testerink’s lab as a postdoc. My current research focuses on the mass spec-based analysis of proteins that function in salt stress signalling. The identification of potential protein targets of phosphatidic acid in Arabidopsis roots under salt stress is leading to new directions of salt stress research (McLoughlin et al. 2013).
Besides research, I enjoy teaching and assisting students.
During my BSc in biology I have always had an interest in both ecology and molecular biology of plants. Soon I found myself happily doing a research project at the Plant eco-physiology group in Utrecht, where I could study the physiological and molecular backgrounds of ecological processes in plants. I have a main interest in the plasticity of plants, enabling them to adapt to a wide range of biotic and abiotic circumstances. For a long time the root system has got very little attention in research on plants adapting to abiotic stress. I really enjoy contributing to increasing this knowledge with my project in the group of Christa Testerink, where I study how plants adapt (lateral) root development to salt stress. Because lateral roots are specialized in water and nutrient uptake, they might also be the place where most sodium is taken up. Because excessive sodium uptake is toxic to the plant, we hypothesize that adapting lateral root development can be favourable for salt tolerance. Previous research of Magdalena Julkowska showed that the root systems of Arabidopsis accessions develops differently and that this is related to the salt tolerance of the accessions. I will continue on this project by investigating what the functionality is of the difference in development and how this is regulated by the plant. Two auxin biosynthesis genes, which are picked up in Magdalena’s study, will be central in this project. For me, this project has the potential to connect the underlying genetics of a physiological process with its function. Eventually, this knowledge will lead to targets for improving crop tolerance to salt stress.
My name is Ruud Korver and I started my PhD in September 2014. I am interested in plant responses to abiotic stress. My role in our group is to focus more on the biochemistry and cell biology behind plant salt stress and in particular halotropism. Using different techniques I get to unravel pieces of the mechanism behind this fascinating phenomenon. This way, I am becoming an all-rounder in the lab. And that is necessary because finding a novel salt tolerance mechanism is one thing, but understanding exactly how it works is where the true challenge lies! Using and learning multiple different molecular tools is what makes my work challenging everyday. But the work environment in our department and especially in our group is excellent and helps me to one day become a molecular salinity tolerance expert!
Personal page: http://www.uva.nl/profile/r.a.korver
Graduated April 30, 2015. UvA-DARE thesis: http://dare.uva.nl/record/1/471032
Now postdoc at KAUST, SA http://saltlab.kaust.edu.sa/Pages/Magdalena-Julkowska.aspx
Graduated Oct 17, 2012. Thesis link UvA DARE
Now postdoc at Vierstra lab, Washington Unversity in St. Louis, USA
Ik ben geïnteresseerd in hoe planten zich aanpassen aan ongunstige omstandigheden. Planten reageren zeer snel en adequaat op veranderingen in hun omgeving. De eerste reactie van een plant bestaat vaak uit het veranderen van de lipiden in de celmembraan. Deze verandering zet vervolgens een cascade aan vervolgreacties in een cel in gang die uiteindelijk leiden tot een betere overleving van de plant. Een sleutelrol is weggelegd voor het alarmmolecuul phosphatidylzuur (PA). Dit lipide wordt gemaakt onder diverse stressvolle omstandigheden, zoals droogte, kou en een aanval van ziekteverwekkers. Van NWO-CW heb ik in 2006 een Vidi-onderzoeksbeurs gekregen om te onderzoeken wat de functie van PA is. Daarvoor werkte ik op een Veni onderzoeksbeurs.
Momenteel richt mijn onderzoek zich op hoe stress de ontwikkeling en groei van een plant stuurt. Zie ook
voor een Nederlandse samenvatting.
Ik geef onderwijs in diverse cursussen in de UvA bachelors Biologie en Biomedische Wetenschappen en in de UvA/VU Master Green Life Sciences. In een grassroots-project voor onderwijsvernieuwing met behulp van ICT, heb ik het gebruik van stemkastjes geïntroduceerd in mijn colleges.