title: A comparative analysis of perturbations caused by a gene knock-out, a dominant negative allele, and a set of peptide aptamers.
abstract: The study of protein function mostly relies on perturbing regulatory networks by acting upon protein expression levels or using transdominant negative agents. Here we used the Escherichia coli global transcription regulator Fur (ferric uptake regulator) as a case study to compare the perturbations exerted by a gene knock-out, the expression of a dominant negative allele of a gene, and the expression of peptide aptamers that bind a gene product. These three perturbations caused phenotypes that differed quantitatively and qualitatively from one another. The Fur peptide aptamers inhibited the activity of their target to various extents and reduced the virulence of a pathogenic E. coli strain in Drosophila. A genome-wide transcriptome analysis revealed that the "penetrance" of a peptide aptamer was comparable to that of a dominant negative allele but lower than the penetrance of the gene knock-out. Our work shows that comparative analysis of phenotypic and transcriptome responses to different types of perturbation can help decipher complex regulatory networks that control various biological processes.
authors.affiliation: Differentiation and Cell Cycle Group, Laboratoire de Biologie Moléculaire de la Cellule, UMR 5239 CNRS/ENS Lyon, Université Lyon 1, Ecole Normale Supérieure de Lyon, IFR 128 BioSciences Lyon-Gerland, 46 allée d'Italie, 69364 Lyon cedex 07, France.
authors.forename: Nadia
authors.initials: N
authors.lastname: Abed
authors.forename: Marc
authors.initials: M
authors.lastname: Bickle
authors.forename: Bernard
authors.initials: B
authors.lastname: Mari
authors.forename: Matthieu
authors.initials: M
authors.lastname: Schapira
authors.forename: Raquel
authors.initials: R
authors.lastname: Sanjuan-España
authors.forename: Karine
authors.initials: K
authors.lastname: Robbe Sermesant
authors.forename: Olivier
authors.initials: O
authors.lastname: Moncorgé
authors.forename: Sandrine
authors.initials: S
authors.lastname: Mouradian-Garcia
authors.forename: Pascal
authors.initials: P
authors.lastname: Barbry
authors.forename: Brian B
authors.initials: BB
authors.lastname: Rudkin
authors.forename: Marie-Odile
authors.initials: MO
authors.lastname: Fauvarque
authors.forename: Isabelle
authors.initials: I
authors.lastname: Michaud-Soret
authors.forename: Pierre
authors.initials: P
authors.lastname: Colas
mesh_terms: D000483:Alleles; D000818:Animals; D052158:Aptamers, Peptide / Q000737:chemistry*; D001483:Base Sequence; D017931:DNA Primers; D004330:Drosophila; D005799:Genes, Dominant; D020798:Two-Hybrid System Techniques