Research of Molecular Biology

Our research includes studies on root and shoot architecture, plant-microbe symbiosis, organ formation, flowering time, tissue regeneration and embryo development. Currently, our research is divided into seven research groups:

• Plant architecture and development
• Nodulation Engineering
• Molecular development of Arbuscular Mycorrhizal symbiosis
• RNA Biology of Plant Embryos
• Plant Photobiology
• The TimES Lab
• Plant photoreceptors and chloroplastic metabolism

How do plants grow? A seemingly simple question, however beneath the surface there is much to learn. Within many of our crops, there is limited knowledge at the molecular level on the development of different yield related organs such as side shoots and seeds in relation to their environment. This knowledge is important, as different yield components are often negatively correlated, which makes optimizing yield in a sustainable way difficult.

The trade-off between yield components is hard to address due to a lack of knowledge on the molecular-genetic networks that control the development of different yield related organs. Key to addressing this knowledge gap is understanding the role of transcriptional regulatory networks, and the natural variation therein, on plant architecture and developmental timing.

Many of our crop species have large genomes and are characterized by extensive gene duplication events that occurred independently in flowering time and plant architecture genes, which has led to diversification in the functions of these genes (sub-and neofunctionalisation).

Studying the role of flowering time and plant architecture genes in plant organ development and developmental timing in model species like Arabidopsis and rice is thus often insufficient to understand their function in other species such as the temperate cereals barley and wheat. Understanding the evolution, functional conservation and divergence of molecular networks that control plant development and architecture are amongst the core research areas of this team.

Our long term goal is to build a solid fundamental understanding of the genes and molecular networks that control plant architecture and development.

Dr.ir.ing. GW (Wilma) van Esse - group leader
PE (Pierangela) Colleoni - PhD student
R (Roman) Lakerveld MSc - PhD student
AJG (Ton) Winkelmolen - PhD student
MV (Marijke) Hartog - Technician

Is it possible to engineer non-leguminous crop plants such that they can establish a nitrogen-fixing nodule symbiosis with rhizobium bacteria? This question was raised already in 1917 by two American researchers. In those days, it was discovered that legume plants, like beans, clovers and peas, possess a unique trait. Legumes can interact with nitrogen-fixing rhizobium bacteria, which results in the formation of new organs on the root of the plant, so-called nodules. Inside nodule cells bacteria are hosted as transient organelle-like structures that convert dinitrogen gas (N₂) into ammonia. This enzymatic reaction is fuelled by carbohydrates derived from the plant. In return, the plant receives ammonia, which allows a nitrogen-rich lifestyle, and growth independent of available nitrogen sources in the soil.

A century of high profile research has uncovered many aspects of the legume – rhizobium mutualistic symbiosis, including the molecular signalling dialogue between both partners, the genetic networks controlling nodule formation and bacterial infection, the biochemistry of nitrogen fixation, and the evolutionary relation of the legume rhizobium symbiosis to other symbiotic interactions.

However, despite all this in-depth knowledge, successful engineering of the nitrogen-fixing nodulation trait has not been achieved. Funded by the Bill & Melinda Gates Foundation, we -together with an international consortium- aim to achieve a breakthrough by providing a proof of concept of engineering nitrogen-fixing root nodules. Thereby in Wageningen the target crop is cassava.

To uncover an evolutionary blueprint of the nitrogen-fixing nodulation trait, we use Parasponia (Cannabis family). The genus Parasponia represents the only non-leguminous plant species that can form nitrogen-fixing nodules with rhizobium. Parasponia and legumes share the evolutionary origin of the nodulation trait, but soon after gaining the capacity to form nodules both lineages evolved independently. By comparing legumes, Parasponia, and non-nodulating sister species, essential symbiosis genes are identified. Subsequently, engineering constructs are designed and tested in cassava and other plant species. To achieve a relatively short “design, built, test cycle” in the engineering strategy, we use synthetic biology, highly specific reporter constructs, and optimized transformation protocols.

Dr. ir. R (Rene) Geurts - group leader
Dr. RHJ (Rik) Huisman - post-doc
Dr. J (Joël) Klein - post-doc
Dr. J (Jieyu) Liu - post-doc
J (Jing) Wang, MSc - PhD-student
CL (Carolien) Franken - technician

To live in environments where nutrients are limited, plants engage in an endosymbiosis with arbuscular mycorrhizal (AM) fungi. These fungi colonize plant roots and are hosted inside root cortex cells, where highly branched hyphal structures called arbuscules are formed (Figure 1). There, the fungi deliver scarce minerals, especially phosphate and nitrogen sources, that they take up from the soil to the plant for which they get sugars and lipids in return.

The AM symbiosis is very ancient and occurs in the vast majority of all land plants, which makes it one of the agriculturally and ecologically most important endosymbioses in plants. Understanding how AM fungi are accommodated inside plant roots and how nutrient exchange is controlled is of major importance as it determines the symbiotic efficiency of the interaction. Therefore, we use molecular, genetic- and cell-biological approaches to study the molecular mechanisms by which AM fungi optimize symbiotic nutrient transfer; both from the plant and the fungal side.

Dr ir. EHM (Erik) Limpens - Group leader
X (Xiaofan) Ma - PhD student

Soon after fertilization of the egg and sperm, the zygotic genome becomes transcriptionally activated in plants and drives a series of coordinated cell divisions and cell-type specific gene regulatory programs to establish the basic plant body plan. Moreover, epigenetic marks associated with gene regulation are re-established across the genome during this early phase of plant life. However, the mechanisms underlying the formation of initial cell types and epigenomic landscapes in early embryos remain to be fully explored, especially in plants.

We currently use Arabidopsis thaliana as a model system to characterize the molecular basis of plant embryogenesis. For example, we perform transcriptomic approaches, including profiling RNA populations from individual cells, to explore how gene expression programs initiate and diversify across emerging embryonic cells that are the precursors to the most fundamental plant cell types.

Our main research focus is on small RNAs, which do not encode proteins and are only 20-24 nucleotides in length. We have found that different groups of small RNAs are required for pattern formation by repressing transcription factors and other key developmental regulators, as well as the re-establishment of DNA methylation genome-wide during embryogenesis. To investigate how different populations of RNA molecules mediate cellular differentiation and (epi)genetic regulation during plant embryogenesis, we also develop and implement various bioinformatic, genomic, genetic and microscopy techniques.

MD (Michael) Nodine, PhD - Group leader
JJ (Job) Dirkmaat, MSc - PhD-student
B (Bowei) Jiang, MSc - PhD-student
MEW (Marije) Vos, MSc - PhD-student

Plants are remarkably flexible towards their environment. They have evolved ways to deal with all sorts of extremities and are able to interpret various combinations of environmental input signals. We study the molecular mechanisms that plants use to process information about their light environment and translate input signals into adaptive developmental responses. This is particularly important for growth at high planting densities, because light becomes scarce and is a resource that plants compete for.

In addition to understanding shade avoidance responses, that guide leaves away from shade, we also investigate how plants balance these responses against responding to other environmental challenges. Molecular mechanisms of signal integration are key in our research! In addition to understanding molecular mechanisms, we also study how these plant behaviours improve (or not) plant performance, growth and yield.

More information about the photobiology team and research is available at plantphotobiology.com.

Prof.dr. R (Ronald) Pierik - Professor/chairholder
L (Leonardo) Jo, PhD - Postdoc
SEA (Sanne) Matton, MSc - PhD student
L (Lisa) Oskam, MSc - PhD student
SS (Siddhant) Shetty, MSc - PhD-student
ARI (Alysha) Somer, MSc - PhD student
KJ (Kyra) van der Velde, MSc - PhD student
RJM (Robert) Winter, MSc - PhD student
Ing. M (Michiel) Lammers - Technician

Plants can tell time. Like most organisms that have adapted to Earth’s ~24h cycle, plants have developed an internal timekeeping mechanism known as the circadian clock, that allows them to predict rhythmic environmental variations and influences their responses to external cues.

Welcome to the Timing of Environmental Signalling (TimES) lab. Our lab is dedicated to unravelling the fascinating relationship between the circadian clock and environmental signals, with a particular focus on understanding how this interaction influences plant plasticity. Through cutting-edge methods spanning different fields of research, we explore how the circadian clock affects the adaptability and resilience of plants. Our work holds significant promise for the field of agriculture, as it sheds light on the potential to improve plant productivity and contribute to crop enhancement programs.

While our primary model organism is the 'workhorse' plant Arabidopsis thaliana, we are also at the forefront of establishing pennycress (Thlaspi arvense) as a translational crop model, thus extending the relevance of our findings to real-world agricultural applications. We are on a journey to unlock the secrets of plant-environment interactions and revolutionise the future of sustainable agriculture.

At the TimES lab, we are firmly committed to fostering an equal, diverse, collaborative, and inclusive environment that enriches our research culture. We believe that the contributions of individuals from all backgrounds and perspectives are key to improving the outcome of our scientific endeavours. We are driven by a passion for scientific discovery, open science and a commitment to addressing critical challenges in agriculture. With a strong foundation in plant biology, phenotyping, genetics, molecular biology, photobiology, bioinformatics and chronobiology, we seek to understand the fundamental mechanisms that govern how plants respond to their environment. Through collaborative research and our expertise in molecular biology, circadian rhythms, genomics, and systems biology, we are at the forefront of pioneering research that seeks to optimise plant responses to varying environmental conditions. Our ultimate goal is to translate the knowledge we gain to fuel advancements in crop improvement programs, contributing to food security and sustainable agriculture. We invite you to explore our lab's exciting work and be a part of our goal to create a sustainable and more productive future.

A (Andres) Romanowski - Group leader
J (Jiancun) Chen - PhD student
N (Nidhi) Mishra, MSc - PhD student

Light photoreceptors, including the Red/Far-Red light and temperature sensing phytochromes (phys) and the blue-light sensing cryptochromes (crys), are master integrators of environmental signals, with an indispensable role in chloroplast development, photosynthetic metabolism and growth.

As population increases, one promising approach to boosting agricultural productivity is using photobiological approaches to improve photosynthetic efficiency and chloroplast metabolism. However, our current understanding of the role of photoreceptors in tuning chloroplast functions, including cellular energy production in a changing environment, remains limited. Our research focuses on dissecting novel mechanistic insights on the photosensory signaling that delivers environmental information for tuning essential chloroplastic pathways, including photosynthesis and the chloroplastic isoprenoid biosynthesis (MEP pathway). By addressing how multi–organellar energy production systems emerged and how they achieve homeostasis, enabling new avenues for plants with enhanced stress resilience, we aim to uncover mechanisms that are critical for life.

We use the model plant Arabidopsis thaliana and tomato together with our expertise in molecular genetics, photo-physiology, biochemistry, cell biology, chloroplast biology and bioinformatics, to go beyond our current understanding of phy/crys function as regulators of transcriptional cascades and address post-transcriptional inter-organellar communication channels, based on RNA binding proteins, to convey light cues for photosynthetic optimization.

My lab also interconnects fundamental and applied photobiology with multidisciplinary studies including natural-social science multinational partnerships, participative science and partnerships with industry and other stakeholders including farmers, traditional cooks, chefs and the public, to address global agricultural challenges related to sustainable agricultural production, nutrition and climate change. Using tomato as a model system we are developing new tools and strategies to unravel photosensory mechanisms of crop resilience to climate change based on ancestral tomato agrodiversity and indigenous agricultural knowledge, concurrently preserving biological resources of immense cultural value and of critical importance for global agriculture - see Tomatoes for Tomorrow for more information.

G (Gabriela) Toledo Ortiz, PhD - Group leader