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.
Claverie
Jean-Michel
JM
Structural and Genetic Information Laboratory, UMR 1889 CNRS-AVENTIS, 31 Chemin Joseph Aiguier, 13402 Marseille, cedex 20, France.
Monchois
Vincent
V
Audic
Stéphane
S
Poirot
Olivier
O
Abergel
Chantal
C
D000890:Anti-Infective Agents; D016503:Drug Delivery Systems; D004353:Drug Evaluation, Preclinical / Q000379:methods; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects; D005798:Genes, Bacterial / Q000187:drug effects*; D016680:Genome, Bacterial
D000890:Anti-Infective Agents