Steven Maere Lab

Research focus

Modeling the evolution of transcriptional systems in silico 
For the past few decades, the field of molecular evolution has largely focused on the evolution of individual gene families and overall genome structure. Analogous to the transition from reductionist to system-scale approaches in molecular biology, the logical next step in molecular evolution research is to study the evolution of genes in the context of the systems in which they function. One way to study how systems of interacting components evolve is to simulate the evolution of suitably abstracted system models in silico. Given recent developments in the field of high-performance computing, it is now possible to simulate the evolution of molecular systems at an unprecedented level of mechanistic detail. We use mathematical models to map the genotype of artificial transcriptional regulatory systems to their expression phenotype. We then use these models in population-scale evolutionary simulations to investigate how transcriptional systems evolve. One of our major research interests is to study how duplicated transcriptional systems diverge. We are particularly interested in unraveling the mechanisms by which dosage-balance constraints on duplicated transcription factors can be resolved over evolutionary time. Many regulatory genes do not duplicate easily on their own, because duplication upsets their dosage balance with other transcription factors or targets. Whole-genome duplication (WGD) on the other hand is thought to preserve dosage balance, and moreover to lead to selective retention of dosage-balance sensitive genes, since their loss after WGD would create a reverse dosage balance effect. As a consequence, post-WGD organisms are endowed with a 'regulatory spandrel’, a collection of regulatory genes that may not immediately add extra functionality but that cannot be purged easily from the genome. It is thought that under the right circumstances, these non-adaptively preserved genes may be co-opted for adaptive innovations, but this requires that the dosage-balance constraints be lifted, and it is currently not clear how this is accomplished.
 
 Profiling individual field-grown plants to reverse engineer plant systems and crosstalk between stress pathways
 To develop crops with enhanced yield and tolerance to field stress conditions, we need to fundamentally change our approach to studying stress response pathways in plants. Most stress studies performed under controlled laboratory conditions are of limited predictive value for phenotypes in the field. In lab conditions, stress responses are usually studied in isolation, whereas in the open environment a multitude of stresses operate in synergistic and antagonistic interaction to modulate plant phenotypes. To get a view on the complex interactions between plant stress response pathways and their effect on yield phenotypes, we aim to harness natural gene expression and phenotype variation among genetically identical field-grown plants, based on the premise that each individual plant is subject to subtle deviations of several micro-environmental factors from the field average. We are currently developing methods to use individual plant datasets for reverse engineering stress response pathways, their interaction and their impact on yield-related phenotypes, focusing on maize and rapeseed as model crops.

Publications

Domestication and Divergence of Saccharomyces cerevisiae Beer YeastsGallone B* Steensels J* Prahl T Soriaga L Saels V Herrera B Merlevede A Roncoroni M Voordeckers K Miraglia L Teiling C Steffy B Taylor M Schwartz A Richardson T White C Baele G Maere S* Verstrepen K*CELL, 166, 1397-1410, 2016* These authors contributed equally
Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundaryVanneste K Baele G Maere S* Van De Peer Y*GENOME RESEARCH, 24, 1334-47, 2014* These authors contributed equally
Modeling the evolution of molecular systems from a mechanistic perspectiveGutierrez Betancur J, Maere STRENDS IN PLANT SCIENCE, 19, 292-303, 2014
Predicting Gene Function from Uncontrolled Expression Variation among Individual Wild-Type Arabidopsis PlantsBhosale R* Jewell J* Hollunder J Koo A Vuylsteke M Michoel T Hilson P Goossens A Howe G Browse J Maere SPLANT CELL, 25, 2865-77, 2013* These authors contributed equally
Reconstruction of Ancestral Metabolic Enzymes Reveals Molecular Mechanisms Underlying Evolutionary Innovation through Gene DuplicationVoordeckers K Brown C Vanneste K Van Der Zande E Voet A Maere S* Verstrepen K*PLOS BIOLOGY, 10, e1001446, 2012* These authors contributed equally

News

Beer yeasts are dogs, wine yeasts are cats

08/09/2016 - Researchers from VIB, KU Leuven and Ghent University found that yeasts used for beer and winemaking have been domesticated in the 16th century, around 100 years before the discovery of microbes.

Reconstruction of prehistoric DNA refutes criticism on theory of evolution

11/12/2012 - Scientists from VIB, KU Leuven, UGent and Harvard have succeeded in reconstructing DNA and proteins from prehistoric yeast cells.

VIB-Ghent University and Bayer CropScience scientists start collaboration to accelerate improvement of agricultural crops

21/09/2011 - Using epigenetics and computational biology, the scientists will develop new molecular breeding tools. The results of the studies will be made public in scientific journals.

From bench to field and back

15/09/2011 - The rapidly growing population, accelerating climate change and a rush on biofuels are pushing plant breeders to look for crops with higher yields. Basic research into plant processes by academic and industrial scientists plays a key role.

Steven Maere

Steven Maere

Research area(s)

Model organism(s)

Bio

​​PhD: VIB-Ghent Univ., Ghent, Belgium, 2006
Visiting Postdoc.: Univ. California, Berkeley, USA, 2008-09
VIB Group leader since October 2009

Contact Info

VIB-UGent Center for Plant Systems BiologyUGent-VIB Research Building FSVMTechnologiepark 927 9052 GENTRoute description
steven.maere@ugent.vib.bePhone: +32 9 331 38 05