Characterization of poplar metabotypes via mass difference enrichment analysis.

Instrumentation technology for metabolomics has advanced drastically in recent years in terms of sensitivity and specificity. Despite these technical advances, data analytical strategies are still in their infancy in comparison with other ‘omics’. Plants are known to possess an immense diversity of secondary metabolites. Typically, more than 70% of metabolomics data are not amenable to systems biological interpretation due to poor database coverage. Here, we propose a new general strategy for mass spectrometry-based metabolomics that incorporates all exact mass features with known sum formulae into the evaluation and interpretation of metabolomics studies. We extend the use of mass differences, commonly used for feature annotation, by re-defining them as variables that reflect the remaining ‘omic’ domains. The strategy uses exact mass difference network analyses exemplified for the metabolomic description of two gray poplar (Populus x canescens) genotypes that differ in their capability to emit isoprene. This strategy established a direct connection between the metabotype and the non-isoprene emitting phenotype, as mass differences pertaining to prenylation reactions were over-represented in non-isoprene emitting poplars. The analysis of mass differences was not only able to grasp the known chemical biology of poplar but it also improved the interpretability of yet unknown biochemical relationships

BAP, a rat liver protein that activates transcription through a promoter element with similarity to the USF/MLTF binding site.

The vitellogenin genes of Xenopus are liver-specifically expressed. An in vitro transcription system derived from rat liver nuclei allowed us to define the cis-element BABS (B-activator binding site) in the promoter of the B1 vitellogenin gene. An oligonucleotide encompassing the region from -53 to -44 linked to a TATA box is sufficient for a tenfold increase of the transcriptional activity. Gel retardation assays with nuclear rat liver proteins reveal two DNA-protein complexes: Complex 1 can be competed by the USF/MLTF binding site of the adeno major late promoter whereas complex 2 is a distinct protein we refer to as BAP (B-activator protein). In vitro transcription experiments in the presence of USF/MLTF binding site as competitor show that BAP is an efficient transcription factor. Based on UV cross-linking we estimate that BAP has a molecular weight of 58 kd. Phosphatase treatment reveals that DNA binding of BAP requires phosphorylation. BABS is also present in the hepatitis B virus enhancer suggesting that it might play a role in the tumorigenic potential of the virus