Science, Engineering and Technology Group

Department of Microbial and Molecular Systems

CENTRE OF MICROBIAL
AND PLANT GENETICS

Research profile

The core activity of the CMPG is to generate and exploit
knowledge on evolution, genetic networks and biochemical
pathways for a selection of bacteria, fungi and plants,
taking into account different environmental conditions.
The experimental systems studied are various bacteria in
relation to plant (e.g.

Azospirillum, Rhizobium, Pseudomonas),

and human health (e.g.

Lactobacillus, Pseudomonas),

Saccharomyces cerevisiae, Candida albicans, Arabidopsis
thaliana and crop plants. The experimental approaches
combine wet lab analysis and computational biology,
aiming for a systems approach by integration of biology,
chemistry, bio-informatics and engineering, exemplified
by the systems microbiology which is strongly developed
in the CMPG.

The research within the CMP is organised in seven subgroups:

Salmonella and Probiotics

The S&P group consists of the Salmonella and Probiotic
subgroups. The Salmonella group studies the molecular
mechanisms of bacterial biofilm formation and the interactions
between (evolving) strains within biofilms. This knowledge
is applied to the development of novel antibiofilm strategies
which have a low likelihood of resistance development.
The Probiotic group investigates the interactions of
gastrointestinal and urogenital probiotic Lactobacillus
strains with the human host and with bacterial/viral (HIV,
HSV-2) pathogens. Another focus is on the development
of recombinant Lactobacillus strains to be used as vaccines.

Plant Growth Promoting Rhizobacteria and
Biodegradation

The main activity within the PGPRB group is dedicated to
the exploration of antagonistic interactions among plant -
associated pseudomonads and related soil bacteria,
mediated by proteins (bacteriocins) or secondary metabolites.
Biosynthesis, structure and the mode of action of active
substances are elucidated using state-of-the-art approaches
in molecular microbiology. In addition to gaining insight in
this aspect of social life of these bacteria, this approach
aims at the identification of novel antibacterials and their
targets suitable to combat pathogens. A second line of
research investigates the adaptive capacity of certain soil
bacteria to degrade agrochemicals, such as herbicides
and insecticides, by characterization of the genes and
biochemical pathways involved.

Plant-Fungi Interactions

Research at PFI resulted in the discovery of several types
of novel antifungal proteins. Pioneering research was
continued on one of them, namely the plant defensins
(PDFs). Primarily based on PDFs studies, research at PFI
was further developed in two distinct research units,
the Plant Unit and the Fungus/Yeast Unit. In the Plant
Unit research is focussed on stress-induced peptides,
including PDFs, and on their role in the plant's resistance
mechanisms to mainly necrotrophic pathogens. Basic studies
in the model plant Arabidopsis thaliana are further translated
to agronimically important crops such as tomato, lettuce,
corn and canola. The Plant Unit is associated with the VIB
Department of Plant systems Biology. In the Fungus/Yeast
Unit research is focussed on the unravelling of the mode
of action of bioative peptides and small molecules including
their antifungal, antibiofilm, antiapoptotic activities. Yeast
models are developed to study diseases of higher eukaryotes
including plants and humans.

Contact

Department of Microbial and Molecular Systems
Centre of Microbial and Plant Genetics
Kasteelpark Arenberg 20 box 2460
3001 LEUVEN, Belgium
www.biw.kuleuven.be/m2s/cmpg

KU Leuven. Inspiring the outstanding.

Symbiotic and Pathogenic Interactions

The SPI group performs molecular microbiological research
both on pathogenic as well as symbiotic bacteria with a
focus on antibiotic-tolerance or persistence, evolutionary
dynamics of adaptation to complex phenotypes and
bacterium-plant interactions. Target bacteria include
Escherichia coli, Pseudomonas aeruginosa, Rhizobium
etli, Staphylococcus aureus and Mycobacterium smegmatis.
At the methodological level, the group pursues in-house
genetic-biochemical approaches combined with high-
throughput genomic analyses (NGS, RNAseq), as well as
advanced microscopic and bioinformatics examinations.
Research is performed both at population and single-cell
levels as well as during interaction with the eukaryotic host
(cellular, plant and animal systems). Our application-oriented
research pipeline is directed towards the discovery of novel
antibacterials which we want to further develop in the
framework of topical applications, anti-biofilm coatings
and controlled release.

Genetics and Genomics

The G&G team investigates how and why living systems
work. In particular, we are intrigued by genetic and epigenetic
regulation, inheritance and evolution. Our research combines
theory and experiment, including molecular biology, genetics,
genomics, bioinformatics, and mathematical modelling.
Most research focuses on the model eukaryote
Saccharomyces cerevisiae (beer yeast), but we are also
venturing into higher eukaryotes, including insects, plants
and humans. Apart from striving for purely scientific insight,
we are also exploring possible applications of our findings,
most notably by optimising yeast strains for the fermentation
industry (beer, wine, bread, chocolate, biofuels etc.).

Computational Systems Biology

This group is interested in understanding biological systems
as a whole and gaining insight into molecular evolution.
This is achieved through computational analysis of complex
molecular data generated by the ever growing number of
new technologies that can systematically measure the
behaviour of multiple cellular components, such as biochemical
activities, biophysical properties, subcellular localization
and interaction. The analyses require both using and
developing new methods to integrate, visualize and query
the large amounts of information available. Selected projects
include analysis of protein mass-spectrometry data to
discover new protein interactions, analysis of mutations

that can affect protein function, assigning functions to
post-translational modifications and the evolutionary
dynamics of protein interaction networks.

Predictive Genetics and Multicellular Systems

Biology has become a data intense and quantitative science,
and advanced analyses of the generated measurements
are important to advance our understanding of fundamental
biological questions. In this group a predominantly
computational approach is taken, in close contact with
experimentation, to advance a range of research topics.
One focus is on whole genome reverse genetic predictions,
in which careful computational modeling of genetic variation
in individuals is used to predict likely phenotypes. A second
focus is on the embryogenesis of C. elegans,. We have
developed a pipeline to retrieve cell positions and divisions
during early embryogenesis and then use this data to
try to advance our understanding of how cells move
autonomously, and interact with their neighbors to guide
cell differentiation.

Keywords

Molecular microbiology

•

plant molecular biology

•

biochemistry

•

biological chemistry

•

physiology

•

bioinformatics

•

systems biology

Unique infrastructure

The Centre of Microbial and Plant Genetics is equipped
with up-to-date instruments for culturing and molecular
analysis of microbial cells, eukaryotic cells and plants
and is developing algorithms and compendia for
computational biology.

Collaboration and users

The Centre of Microbial and Plant Genetics participates
with European (FP6, FP7), Belgian Federal (IUAP-PAI) and
Flemish (Programme Financing, BOF) authorities; Flemish
Research Agencies (FWO, IWT, VIB, Odysseus, Hercules,
VLIR-UOS); industries (food and beer, plant and human
health sector, pharma, agrochemical).