title: A strategy to retrieve the whole set of protein modules in microbial proteomes.
abstract: Protein homology is often limited to long structural segments that we have previously called modules. We describe here a suite of programs used to catalog the whole set of modules present in microbial proteomes. First, the Darwin AllAll program detects homologous segments using thresholds for evolutionary distance and alignment length, and another program classifies these modules. After assembling these homologous modules in families, we further group families which are related by a chain of neighboring unrelated homologous modules. With the automatic analysis of these groups of families sharing homologous modules in independent multimodular proteins, one can split into their component parts many fused modules and/or deduce by logic more distant modules. All detected and inferred modules are reassembled in refined families. These two last steps are made by a unique program. Eventually, the soundness of the data obtained by this experimental approach is checked using independent tests. To illustrate this modular approach, we compared four proteobacterial proteomes (Campylobacter jejuni, Escherichia coli, Haemophilus influenzae, and Helicobacter pylori). It appears that this method might retrieve from present-day proteins many of the modules which can help to trace back ancient events of gene duplication and/or fusion.
authors.affiliation: Evolution Moléculaire et Génomique, Institut de Génétique et Microbiologie, Université Paris-Sud, 91405 Orsay Cedex, France.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Le Bouder-Langevin
authors.forename: Isabelle
authors.initials: I
authors.lastname: Capron-Montaland
authors.forename: Renaud
authors.initials: R
authors.lastname: De Rosa
authors.forename: Bernard
authors.initials: B
authors.lastname: Labedan
mesh_terms: D001426:Bacterial Proteins / Q000145:classification / Q000235:genetics*; D016123:Campylobacter jejuni / Q000235:genetics; D030562:Databases, Protein; D029968:Escherichia coli Proteins / Q000235:genetics; D019143:Evolution, Molecular; D020440:Gene Duplication; D005798:Genes, Bacterial / Q000235:genetics*; D006090:Gram-Negative Bacteria / Q000235:genetics*; D006193:Haemophilus influenzae / Q000235:genetics; D016480:Helicobacter pylori / Q000235:genetics; D020543:Proteome / Q000235:genetics*; D011995:Recombination, Genetic / Q000235:genetics; D012107:Research Design / Q000592:standards; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D020543:Proteome