Biomedical subjects

Olivier Poirot

Publications and source records attributed to Olivier Poirot.

8 recordsLinked to original sources

PubMed2004

Selective regulation of acid-sensing ion channel 1 by serine proteases.

Acid-sensing ion channels (ASICs) are neuronal Na(+) channels that belong to the epithelial Na(+) channel/degenerin family. ASICs are transiently activated by a rapid drop in extracellular pH. Conditions of low extracellular pH, such as ischemia and inflammation in which ASICs are thought to be active, are accompanied by increased protease activity. We show here that serine proteases modulate the function of ASIC1a and ASIC1b but not of ASIC2a and ASIC3. We show that protease exposure shifts the pH dependence of ASIC1a activation and steady-state inactivation to more acidic pH. As a consequence, protease exposure leads to a decrease in current response if ASIC1a is activated by a pH drop from pH 7.4. If, however, acidification occurs from a basal pH of approximately 7, protease-exposed ASIC1a shows higher activity than untreated ASIC1a. We provide evidence that this bi-directional regulation of ASIC1a function also occurs in neurons. Thus, we have identified a mechanism that modulates ASIC function and may allow ASIC1a to adapt its gating to situations of persistent extracellular acidification.

Animals↗

PubMed2004

Phydbac2: improved inference of gene function using interactive phylogenomic profiling and chromosomal location analysis.

Phydbac (phylogenomic display of bacterial genes) implemented a method of phylogenomic profiling using a distance measure based on normalized BLAST scores. This method was able to increase the predictive power of phylogenomic profiling by about 25% when compared to the classical approach based on Hamming distances. Here we present a major extension of Phydbac (named here Phydbac2), that extends both the concept and the functionality of the original web-service. While phylogenomic profiles remain the central focus of Phydbac2, it now integrates chromosomal proximity and gene fusion analyses as two additional non-similarity-based indicators for inferring pairwise gene functional relationships. Moreover, all presently available (January 2004) fully sequenced bacterial genomes and those of three lower eukaryotes are now included in the profiling process, thus increasing the initial number of reference genomes (71 in Phydbac) to 150 in Phydbac2. Using the KEGG metabolic pathway database as a benchmark, we show that the predictive power of Phydbac2 is improved by 27% over the previous version. This gain is accounted for on one hand, by the increased number of reference genomes (11%) and on the other hand, as a result of including chromosomal proximity into the distance measure (16%). The expanded functionality of Phydbac2 now allows the user to query more than 50 different genomes, including at least one member of each major bacterial group, most major pathogens and potential bio-terrorism agents. The search for co-evolving genes based on consensus profiles from multiple organisms, the display of Phydbac2 profiles side by side with COG information, the inclusion of KEGG metabolic pathway maps the production of chromosomal proximity maps, and the possibility of collecting and processing results from different Phydbac queries in a common shopping cart are the main new features of Phydbac2. The Phydbac2 web server is available at http://igs-server.cnrs-mrs.fr/phydbac/.

Artificial Gene Fusion↗

PubMed2004

3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment.

This paper presents 3DCoffee@igs, a web-based tool dedicated to the computation of high-quality multiple sequence alignments (MSAs). 3D-Coffee makes it possible to mix protein sequences and structures in order to increase the accuracy of the alignments. Structures can be either provided as PDB identifiers or directly uploaded into the server. Given a set of sequences and structures, pairs of structures are aligned with SAP while sequence-structure pairs are aligned with Fugue. The resulting collection of pairwise alignments is then combined into an MSA with the T-Coffee algorithm. The server and its documentation are available from http://igs-server.cnrs-mrs.fr/Tcoffee/.

Internet↗

PubMed2004

Agonist-independent modulation of N-type calcium channels by ORL1 receptors.

We have investigated modulation of voltage-gated calcium channels by nociceptin (ORL1) receptors. In rat DRG neurons and in tsA-201 cells, nociceptin mediated a pronounced inhibition of N-type calcium channels, whereas other calcium channel subtypes were unaffected. In tsA-201 cells, expression of N-type channels with human ORL1 resulted in a voltage-dependent G-protein inhibition of the channel that occurred in the absence of nociceptin, the ORL1 receptor agonist. Consistent with this observation, native N-type channels of small nociceptive dorsal root ganglion (DRG) neurons also had tonic inhibition by G proteins. Biochemical characterization showed the existence of an N-type calcium channel-ORL1 receptor signaling complex, which efficiently exposes N-type channels to constitutive ORL1 receptor activity. Calcium channel activity is thus regulated by changes in ORL1 receptor expression, which provides a possible molecular mechanism for the development of tolerance to opioid receptor agonists.

Animals↗

PubMed2003

Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments.

This paper presents Tcoffee@igs, a new server provided to the community by Hewlet Packard computers and the Centre National de la Recherche Scientifique. This server is a web-based tool dedicated to the computation, the evaluation and the combination of multiple sequence alignments. It uses the latest version of the T-Coffee package. Given a set of unaligned sequences, the server returns an evaluated multiple sequence alignment and the associated phylogenetic tree. This server also makes it possible to evaluate the local reliability of an existing alignment and to combine several alternative multiple alignments into a single new one. Tcoffee@igs can be used for aligning protein, RNA or DNA sequences. Datasets of up to 100 sequences (2000 residues long) can be processed. The server and its documentation are available from: http://igs-server.cnrs-mrs.fr/Tcoffee/.

Consensus Sequence↗

PubMed2003

Phydbac (phylogenomic display of bacterial genes): An interactive resource for the annotation of bacterial genomes.

Phydbac is a web interactive resource based on phylogenomic profiling, designed to help microbiologists to annotate bacterial proteins. Phylogenomic annotation is based on the assumption that functionally linked protein-coding genes must evolve in a coordinated manner. The detection of subsets of co-evolving genes within a given genome involves the computation of protein sequence conservation profiles across a spectrum of microbial species, followed by the identification of significant pairwise correlations between them. Many ongoing studies are devoted to the problem of computing the most biologically significant phylogenomic profiles and how best identifying clusters of 'functionally interacting' genes. Here we introduce a web tool, Phydbac, allowing the dynamic construction of phylogenomic profiles of protein sequences of interest and their interactive display. In addition, Phydbac can identify Escherichia coli proteins exhibiting the evolution pattern most similar to arbitrary query protein sequences, hence providing functional hints for open reading frames (ORFs) of hypothetical or unknown function. The phylogenomic profiles of all E.coli K-12 protein-coding genes are pre-computed, allowing queries about E.coli genes to be answered instantaneously. The profiles and phylogenomic neighborhoods are computed using an original method shown to perform better than previous ones. An extension of Phydbac, including precomputed profiles for all available bacterial genomes (including major pathogens) will soon be available. Phydbac can be accessed at: http://igs-server.cnrs-mrs.fr/phydbac/.

Bacterial Proteins↗

PubMed2003

Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets.

With more than 100 antibacterial drugs at our disposal in the 1980's, the problem of bacterial infection was considered solved. Today, however, most hospital infections are insensitive to several classes of antibacterial drugs, and deadly strains of Staphylococcus aureus resistant to vancomycin--the last resort antibiotic--have recently begin to appear. Other life-threatening microbes, such as Enterococcus faecalis and Mycobacterium tuberculosis are already able to resist every available antibiotic. There is thus an urgent, and continuous need for new, preferably large-spectrum, antibacterial molecules, ideally targeting new biochemical pathways. Here we report on the progress of our structural genomics program aiming at the discovery of new antibacterial gene targets among evolutionary conserved genes of uncharacterized function. A series of bioinformatic and comparative genomics analyses were used to identify a set of 221 candidate genes common to Gram-positive and Gram-negative bacteria. These genes were split between two laboratories. They are now submitted to a systematic 3-D structure determination protocol including cloning, protein expression and purification, crystallization, X-ray diffraction, structure interpretation, and function prediction. We describe here our strategies for the 111 genes processed in our laboratory. Bioinformatics is used at most stages of the production process and out of 111 genes processed--and 17 months into the project--108 have been successfully cloned, 103 have exhibited detectable expression, 84 have led to the production of soluble protein, 46 have been purified, 12 have led to usable crystals, and 7 structures have been determined.

Acid Anhydride Hydrolases↗

PubMed2002

In Ssarch of new anti-bacterial target genes: a comparative/structural genomics approach.

We outline a joint academic/industrial (CNRS/AVENTIS) functional genomics project aiming at the discovery of new anti-bacterial gene targets. Starting from all publicly available bacterial genomes, a subset of the most evolutionary conserved protein-coding genes has been identified. We retained genes with clear homolog in E. coli and at least one gram-positive bacterium among B.subtilis, M. tuberculosis, L. lactis or S. pyogenes. This subset was further reduced to genes encoding non-membrane proteins of unknown or hypothetical functions. The 221 E. coli Open Reading Frames (ORFs) identified through this comprehensive bioinformatic analysis are now submitted to a systematic 3-D structure determination protocol including cloning, protein expression and purification, crystallisation and X-ray diffraction. Our strategy was designed to focus on promising wide-spectrum targets as well as original biochemical pathways. Bioinformatics is used throughout all phases of project, including the initial large-scale comparative genomics analyses, the purification/expression and crystallisation stages for the detection of helpful sequence-specific features (e.g. cofactor binding motifs, non-structured N- or C- term extremities, etc ), and finally for the interpretation of the structures in conjunction with multiple sequence alignments for the identification of key residues, interaction areas on molecular surfaces, and overall function predictions.

Anti-Infective Agents↗