Biomedical subjects

Arne Müller

Publications and source records attributed to Arne Müller.

5 recordsLinked to original sources

PubMed2005

A ToxR-based two-hybrid system for the detection of periplasmic and cytoplasmic protein-protein interactions in Escherichia coli: minimal requirements for specific DNA binding and transcriptional activation.

The Vibrio cholerae transcriptional regulator ToxR is anchored in the cytoplasmic membrane by a single transmembrane segment, its C-terminal domain facing the periplasm. Most of its N-terminal cytoplasmic domain shares sequence similarity with the winged helix-turn-helix (wHTH) motif of OmpR-like transcriptional regulators. In the heterologous host Escherichia coli ToxR activates transcription at the V.cholerae ctx promoter in a dimerization-dependent manner, which has led to its employment as a genetic indicator for protein-protein interactions. However, although offering a broader potential application range than other prokaryotic two-hybrid systems described to date, ToxR has so far only been used to study interactions between heterologous transmembrane segments or to monitor homodimerization of C-terminal fusion partners in the periplasm and the cytoplasm of E.coli. Here we show that the ToxR-system also allows the detection of heterodimerization in both cellular compartments of E.coli. In addition, to better understand ToxR's mode of action at ctx in E.coli, we have investigated the minimal requirements for its function as a transcriptional activator. We show that the wHTH motif of ToxR's N-terminal domain constitutes the minimal structural element required to activate transcription at ctx in E.coli when fused to a dimerizing protein module.

Bacterial Proteins↗

PubMed2005

Laboratory variability does not preclude identification of biological functions impacted by hydroxyurea.

The multi-lab International Life Sciences Institute (ILSI) project on the application of genomics to risk assessment offered the unique opportunity to investigate the influence of variability within and between laboratories on identifying biologically relevant gene expression changes. We assessed the gene expression profiles of mouse lymphoma L5178Y cells treated with hydroxyurea (HU) in three independent studies from two different laboratories, Sanofi Aventis and Procter and Gamble. Cells were dosed for 4 hr and harvested immediately at the end of the treatment or after a 20-hr recovery period. Cytotoxicity and genotoxicity were evaluated by standard assays. Statistical analysis of these data revealed that, while gene expression responses to HU treatment were markedly different at 4 hr vs. 24 hr, there was otherwise a consistent pattern of dose-response across the three studies. Therefore, the studies were merged and each time point was evaluated separately. At 4 hr, we identified 173 (P < 0.0001) dose-responsive genes with a common trend in all three studies. These were mainly associated with the cell cycle, DNA repair and DNA metabolism, and in particular, the intra-S and G2/M phase checkpoints. At 24 hr, we identified 434 dose-responsive genes common across studies. These genes were involved in lymphocyte-specific activities and the activation of apoptosis via the caspase cascade. Our results show that despite inter-laboratory variability, combining the three studies in a single statistical analysis identifies more significantly-modulated genes than in any of the individual studies, due to improved statistical sensitivity. The genes identified in our study provide information that is relevant to HU biology.

Animals↗

PubMed2004

Clustering of protein domains in the human genome.

We present a systematic study of the clustering of genes within the human genome based on homology inferred from both sequence and structural similarity. The 3D-Genomics automated proteome annotation pipeline () was utilised to infer homology for each protein domain in the genome, for the 26 superfamilies most highly represented in the Structural Classification Of Proteins (SCOP) database. This approach enabled us to identify homologues that could not be detected by sequence-based methods alone. For each superfamily, we investigated the distribution, both within and among chromosomes, of genes encoding at least one domain within the superfamily. The results indicate a diversity of clustering behaviours: some superfamilies showed no evidence of any clustering, and others displayed significant clustering either within or among chromosomes, or both. Removal of tandem repeats reduced the levels of clustering observed, but some superfamilies still displayed highly significant clustering. Thus, our study suggests that either the process of gene duplication, or the evolution of the resulting clusters, differs between structural superfamilies.

Cadherins↗

PubMed2004

3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes.

The 3D-GENOMICS database (http://www.sbg.bio. ic.ac.uk/3dgenomics/) provides structural annotations for proteins from sequenced genomes. In August 2003 the database included data for 93 proteomes. The annotations stored in the database include homologous sequences from various sequence databases, domains from SCOP and Pfam, patterns from Prosite and other predicted sequence features such as transmembrane regions and coiled coils. In addition to annotations at the sequence level, several precomputed cross- proteome comparative analyses are available based on SCOP domain superfamily composition. Annotations are available to the user via a web interface to the database. Multiple points of entry are available so that a user is able to: (i) directly access annotations for a single protein sequence via keywords or accession codes, (ii) examine a sequence of interest chosen from a summary of annotations for a particular proteome, or (iii) access precomputed frequency-based cross-proteome comparative analyses.

Amino Acid Sequence↗

PubMed2002

Structural characterization of the human proteome.

This paper reports an analysis of the encoded proteins (the proteome) of the genomes of human, fly, worm, yeast, and representatives of bacteria and archaea in terms of the three-dimensional structures of their globular domains together with a general sequence-based study. We show that 39% of the human proteome can be assigned to known structures. We estimate that for 77% of the proteome, there is some functional annotation, but only 26% of the proteome can be assigned to standard sequence motifs that characterize function. Of the human protein sequences, 13% are transmembrane proteins, but only 3% of the residues in the proteome form membrane-spanning regions. There are substantial differences in the composition of globular domains of transmembrane proteins between the proteomes we have analyzed. Commonly occurring structural superfamilies are identified within the proteome. The frequencies of these superfamilies enable us to estimate that 98% of the human proteome evolved by domain duplication, with four of the 10 most duplicated superfamilies specific for multicellular organisms. The zinc-finger superfamily is massively duplicated in human compared to fly and worm, and occurrence of domains in repeats is more common in metazoa than in single cellular organisms. Structural superfamilies over- and underrepresented in human disease genes have been identified. Data and results can be downloaded and analyzed via web-based applications at http://www.sbg.bio.ic.ac.uk.

Algorithms↗