The Laboratory of Microbiology investigates biotransformations of
micro-organisms (Archaea, Bacteria, Eukarya) by an integration of physiology,
biochemistry, genetics and bio-informatics. In the Bacterial Genetics research group, molecular techniques are applied
to gain insight in the biochemical and genetic adaptation of selected
processes in distinct model Archaea and Bacteria: (i) thermophilic archaea, (ii)
bacteria that degrade biomass and produce bio-fuels, and (iii) bacteria that
degrade toxic, halogenated compounds. The focus of the ongoing research
projects is on:
-
enzymes
- gene identification & prediction; gene expression; protein purification
& characterization; functional optimization by random & rational
engineering;
-
pathways
- characterization; directed metabolic engineering;
-
regulation
– structure-function analysis of regulators; characterize control at
transcription, translation & protein level;
-
genomics-
comparative & functional genomics (transcriptome / proteome / metabolome
);
Comparative
genomics of available archaeal
genomes has resulted in insight in genome flexibility, and the concerted gain
and loss of gene-clusters. Ongoing projects focus on improved functional
prediction and subsequent biochemical analysis of hypothetical genes,
focussing on gaps in central metabolic pathways and on key transcriptional
regulators. Metabolic engineering is an obvious goal in the near future.
Structure-function
relations of enzymes are addressed in laboratory evolution and rational (computational)
design studies, on the one hand to get insight in the molecular basis of
protein stability and substrate specificity, and on the other hand to attempt
to optimize enzymes for specific applications, including bio-sensors.
Regulation
of
key metabolic features
is addressed in several ongoing studies. In these analyses a wide variety of
biochemical analyses is crucial: in
vitro transcription, footprinting, crystallization, mutagenesis, analysis
of protein-protein interactions, micro array analysis, proteomics.
Goals
The described research is primarily driven by our curiosity to reveal the
molecular basis of selected microbial processes, by using a combination of in
silico and experimental approaches. The long-term motivation to study these unique
features is gaining insight in the functioning of key metabolic features, and
their application in biotechnological processes in (i) agro-food & pharma industry,
(ii) biofuel production, and (iii) the bio-remediation of polluted environments.