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Molecular Plant Biology

The Laboratory of Molecular Plant Biology studies the molecular biology and physiology of plant growth, development and stress tolerance. A long-term objective is  crop optimization. Therefore, we perform basic research in model organisms and apply this knowledge to crop species, food and biodiversity research. This translates into three major lines of research. First, we study the metabolism and role of sugars (e.g. sucrose and fructans) and the role of the natural sweetener stevioside with applications in food (novel prebiotics) and plant stress tolerance (Prof. Dr. Ir. Wim Van den Ende). Second, we study the molecular mechanisms of sugar and stress signaling and how these control plant growth, development and stress tolerance (Prof. Dr. Filip Rolland). Third, we investigate plant developmental regulation to better understand the biodiversity of plants and improve crop performance (Prof. Dr. Koen Geuten).

Prof. Wim Van den Ende : Sugar metabolism group

Fructan and RFO metabolism in plants

Fructans are water-soluble fructose-based polysaccharides that are becoming increasingly popular as health-improving compounds (prebiotics). RFOs are galactosyl extensions of sucrose. Both fructans and RFOs occur in a diverse array of higher plant species,  where they are derived from sucrose. Their metabolism and function are being intensively investigated. The goal is to unravel the physiological functions of fructans and RFOs in plants, and to understand their benefits over starch and sucrose. A  multidisciplinary approach is used , including chemical characterization, purification, localization and characterization of enzymes as  well as analysis of gene expression and regulation.      

It is believed that fructans and RFOs can contribute to drought and frost tolerance. Engineering their metabolism in edible parts of the world crops (e.g., rice) would not only increase the stress tolerance of these crops but also allow these healthy compounds to be cheaply disseminated world-wide. 

Structure - function analysis on family 32 of glycoside hydrolases

In plants, close relationships at the biochemical, molecular and structural levels are found between fructan biosynthesizing and degrading enzymes on the one hand, and acid invertases on the other hand. All these enzymes belong to family 32 of the glycoside hydrolases (GH 32; Plant invertases fullfil crucial roles during growth and development. These enzymes interfere with sugar transport and sugar signalling, as such they influence carbohydrate partitioning and determine crop quality and crop yield (biomass production).

Nevertheless, a tremendous variation in donor and acceptor substrate specificities is observed among the plant GH32 enzymes. To explain these substrate specificities at the molecular level, it is necessary to resolve the crystal structures of complexes formed between the enzymes and their different substrates and to study enzymes mutated in specific amino acid residues. These fundamental insights could contribute to the development of new and better enzymes for specific agronomical and industrial applications.

“Alternative sugars as signals”, “sugars as antioxidants” and “sweet immunity”: emerging new concepts  at  the interfase of sugar and oxidative stress (signaling) pathways

Besides the classic water soluble sugars glucose, fructose and sucrose, with their well-know signaling functions, recent data strongly suggest that  other  plant-derived saccharides (fructans, RFOs etc.) could be involved in signaling processes  and/or  in direct ROS scavenging mechanisms.  Such mechanisms  might counteract  oxidative stress  associated with biotic and/or abiotic stresses. 

It is particularly challenging to further investigate  how vacuolar antioxidant mechanisms could potentially contribute to overall ROS homeostasis in plant cells.

Prof. Filip Rolland : Metabolic signaling group

Plants support life on earth with their unique ability to produce sugars and oxygen by solar energy-driven photosynthesis but they are constantly challenged with changing environmental conditions. As sessile organisms, they largely depend on the ability to accurately monitor and adapt to these changes for optimal growth and survival. The SnRK1 protein kinases (orthologs of yeast SNF1 and mammalian AMPK, a major drug target in metabolic disease and cancer) act as evolutionarily conserved ‘fuel gauges’, triggering a massive reprogramming of transcription in response to diverse stress conditions. Our group is interested in elucidating the SnRK1 signaling pathway and its role in controlling plant metabolism, development and stress tolerance in Arabidopsis thaliana and crop species. We focus on (i) the different (upstream) molecular mechanisms controlling SnRK1 activity in response to metabolic status, (ii) the (downstream) transcriptional and post-transcriptional mechanisms involved in SnRK1-regulation of primary and secondary metabolism (flavonoid biosynthesis), (iii) the role of metabolic gradients and cell-autonomous SnRK1 signaling in the control of leaf growth and development and (iv) the role and mechanisms of SnRK1 signaling in plant stress tolerance and defense.

Prof. Koen Geuten : Evolution and development group

Molecular Evolution of plant development

Our research aims to understand plant biodiversity through comparison of gene regulatory mechanisms between different species. To make sense of the comparisons and as an evolutionary point of reference, we use ancestral sequences that we resurrect through gene synthesis. As a case in point, we focus on MADS-box genes, which are important transcriptional regulators of reproductive plant development. A subsidiary goal of our research is to develop methods that help translating knowledge from model species to crop species.

We currently work on four topics that have unexpected connections between them:

Evolution of epigenetic temperature memory in Brachypodium: Philip Ruelens, Neha Sharma, Niklas Dochy

Brachypodium distachyon is a new model for temperate cereals. In this project we investigate the role of MADS-box genes in the evolution of the regulation of flowering time.

Collaborators: Kerstin Kaufmann (Potzdam University, DE)

Evolution of network topology after whole genome duplication: Zhicheng Zhang, Heleen Coenen, Philip Ruelens

The MADS-box gene family has been amplified in evolution through rounds of whole genome duplication. We resurrect ancestral sequences immediately before and after whole genome duplication to understand whether and how the MADS-domain protein interaction network evolved through these genome wide events.

Collaborators: Yves Van de Peer (Plant Systems Biology, BE), Aalt-Jan Van Dijk (Wageningen University, NL)

Evolution of developmental timing: Heleen Coenen, Tom Stas.

Heterochronic evolution has long been considered the most important mechanism in developmental evolution. However, only recently has the pathway that controls developmental timing been elucidated in plants. Like in the animal model model Caenorabditis, the pathway involves the sequential action of two micrRNA’s and the transcription factors they target. We study the diversity of the regulation of this heterochronic pathway to identitfy cases of heterochronic evolution in plants.

Collaboration: Tom Viaene (Plant Systems Biology, BE), Michiel Vanden Bussche (ENS Lyon, FR)

Predicting MADS protein function from sequence: Tareq Al Hindi, Hannah Degroote

Under development.