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Molecular & Cellular Proteomics 6:2110-2121, 2007.
© 2007 by The American Society for Biochemistry and Molecular Biology, Inc.

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Research

A Comparative Analysis of Perturbations Caused by a Gene Knock-out, a Dominant Negative Allele, and a Set of Peptide Aptamers^*,S

Nadia Abed^,, Marc Bickle^¶, Bernard Mari^||, Matthieu Schapira^¶, Raquel Sanjuan-España, Karine Robbe Sermesant^||, Olivier Moncorgé^¶, Sandrine Mouradian-Garcia, Pascal Barbry^||, Brian B. Rudkin, Marie-Odile Fauvarque^**, Isabelle Michaud-Soret^, and Pierre Colas^,¶,

From the 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, CNRS UMR 5249 Laboratoire de Chimie et Biologie des Métaux and ^** INSERM U873, Laboratoire de transduction du signal, Commissariat à l’Energie Atomique (CEA), Direction des Sciences du Vivant (DSV), l’Institut de Recherches en Technologies et Sciences pour le Vivant (iRTSV), Université Joseph Fourier, 17 avenue des martyrs, Grenoble F-38054 cedex 9, France, ^¶ Aptanomics, 181-203 avenue Jean Jaurès, 69007 Lyon, France, and ^|| CNRS UMR 6097, Institut de Pharmacologie Moléculaire et Cellulaire, University of Nice Sophia Antipolis, 660 Route des Lucioles, F-06560 Sophia Antipolis, France

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.

To whom correspondence may be addressed: CNRS UPS 2682, Station Biologique, B. P. 74, 29682 Roscoff, France. Tel.: 33-2-98-29-23-22; Fax: 33-2-98-29-25-26; E-mail: colas{at}sb-roscoff.fr

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