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Design and validation of a partial-genome microarray for transcriptional profiling of the Bradyrhizobium japonicum symbiotic gene region

Hauser, F. ; Lindemann, A. ; Vuilleumier, S. ; Patrignani, A. ; Schlapbach, R. ; Fischer, H.M. ; Hennecke, H.

In: Molecular Genetics and Genomics, 2006, vol. 275, no. 1, p. 55-67

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    Titre
    • Design and validation of a partial-genome microarray for transcriptional profiling of the Bradyrhizobium japonicum symbiotic gene region
    Auteur
    • Hauser, F.. Institute of Microbiology, Eidgenössische Technische Hochschule, ETH-Hönggerberg, Wolfgang-Pauli-Strasse 10, CH-8093, Zürich, Switzerland
    • Lindemann, A.. Institute of Microbiology, Eidgenössische Technische Hochschule, ETH-Hönggerberg, Wolfgang-Pauli-Strasse 10, CH-8093, Zürich, Switzerland
    • Vuilleumier, S.. Dynamique, Evolution et Expression de Génomes de Microorganismes, FRE 2326 ULP-CNRS, Université Louis Pasteur, 28 rue Goethe, 67083, Strasbourg Cedex, France
    • Patrignani, A.. Functional Genomics Center Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
    • Schlapbach, R.. Functional Genomics Center Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
    • Fischer, H.M.. Institute of Microbiology, Eidgenössische Technische Hochschule, ETH-Hönggerberg, Wolfgang-Pauli-Strasse 10, CH-8093, Zürich, Switzerland
    • Hennecke, H.. Institute of Microbiology, Eidgenössische Technische Hochschule, ETH-Hönggerberg, Wolfgang-Pauli-Strasse 10, CH-8093, Zürich, Switzerland
    Type de document
    • Postprint
    Langue
    • Anglais
    Publié dans
    • Molecular Genetics and Genomics, 2006, vol. 275, no. 1, p. 55-67. Springer-Verlag
    Autre version électronique
    Identifiant OAI-PMH
    • oai:doc.rero.ch:315312
    Summary
    The design and use of a pilot microarray for transcriptome analysis of the symbiotic, nitrogen-fixing Bradyrhizobium japonicum is reported here. The custom-synthesized chip (Affymetrix GeneChip®) features 738 genes, more than half of which belong to a 400-kb chromosomal segment strongly associated with symbiosis-related functions. RNA was isolated following an optimized protocol from wild-type cells grown aerobically and microaerobically, and from cells of aerobically grown regR mutant and microaerobically grown nifA mutant. Comparative microarray analyses thus revealed genes that are transcribed in either a RegR- or a NifA-dependent manner plus genes whose expression depends on the cellular oxygen status. Several genes were newly identified as members of the RegR and NifA regulons, beyond genes, which had been known from previous work. A comprehensive transcription analysis was performed with one of the new RegR-controlled genes (id880). Expression levels determined by microarray analysis of selected NifA- and RegR-controlled genes corresponded well with quantitative real-time PCR data, demonstrating the high complementarity of microarray analysis to classical methods of gene expression analysis in B. japonicum. Nevertheless, several previously established members of the NifA regulon were not detected as transcribed genes by microarray analysis, confirming the potential pitfalls of this approach also observed by other authors. By and large, this pilot study has paved the way towards the genome-wide transcriptome analysis of the 9.1-Mb B. japonicum genome