Characterizing transcription factor families (1) and the development of a generic strategy to identify regulatory units(2) in Lactobacillus plantarum

Title: Characterizing transcription factor families (1) and the development of a generic strategy to identify regulatory units(2) in Lactobacillus plantarum

Description

Supervisors: Mark de Been, Michiel Wels, Christof Francke


IIntroduction:
The integration of hundreds of enzymatic reactions into a metabolic network and the complex response of such a network to environmental changes requires global regulation at the level of enzyme activity and gene transcription. For instance, a bacterium that is confronted with changes in the supply of nutrients can adapt its metabolic potential through the induction of specific catabolic operons (most often induced by the substrate). More permanent changes may require global adaptation and therefore the induction of complete regulons. In general, these ‘longer term’ cellular responses are initiated by transcription factors (TFs).

Project:
One of our groups objectives is the reconstruction of the regulatory network of our model organism the lactic acid bacterium L. plantarum from genomic data. We have two running projects related to this effort:
1) The detailed reconstruction of all regulatory interactions for specific TF families (at present GntR).
2) The design and application of a generic and general approach to reduce the amount of time needed to perform 1) for all TF families.

Methods:
Most TFs consist of two domains. The input domain binds a specific metabolite (signal). Binding of the signal induces conformational changes in the protein often causing dimerization (or dissociation) and resulting in increased (or decreased) affinity of the output domain (i.e. DNA-binding domain) for the binding site on the DNA. We consider separate analysis of the functionality of both domains essential to a successful reconstruction:
- A combination of sequence comparisons, phylogeny, conservation of gene context and analysis of published knowledge will be used to link substrates that induce known TF activity to the TFs that we study, or more precisely, to the substrate binding domain of those TFs.    (input side)
- Simultaneously, conservation of gene context will be used to identify potential TF binding regions. These regions will be searched for TF specific binding motifs using MEME and the resulting motifs will be used to establish putative regulons using MAST.  (output side)
- Next, a strategy will be developed to overlay the regulon predictions with available transcriptome data in order to strengthen the predictions.

The operon prediction made earlier within our group will be used as a starting point for our general approach