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Extracting biological information from DNA arrays: an unexpected link between arginine and methionine metabolism in Bacillus subtilis

Agnieszka Sekowska1, Stephane Robin2, Jean-Jacques Daudin2, Alain Henaut3 and Antoine Danchin14*

Author Affiliations

1 Hong Kong University Pasteur Research Center, Pokfulam, Hong Kong

2 Institut National Agronomique Paris-Grignon, 75231 Paris Cedex 05, France

3 Genome and Informatics, Universite de Versailles-Saint-Quentin, 78035 Versailles Cedex, France

4 Genetics of Bacterial Genomes, Institut Pasteur, 75724 Paris Cedex 15, France

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Genome Biology 2001, 2:research0019-research0019.12  doi:10.1186/gb-2001-2-6-research0019

Published: 1 June 2001

Abstract

Background

In global gene expression profiling experiments, variation in the expression of genes of interest can often be hidden by general noise. To determine how biologically significant variation can be distinguished under such conditions we have analyzed the differences in gene expression when Bacillus subtilis is grown either on methionine or on methylthioribose as sulfur source.

Results

An unexpected link between arginine metabolism and sulfur metabolism was discovered, enabling us to identify a high-affinity arginine transport system encoded by the yqiXYZ genes. In addition, we tentatively identified a methionine/methionine sulfoxide transport system which is encoded by the operon ytmIJKLMhisP and is presumably used in the degradation of methionine sulfoxide to methane sulfonate for sulfur recycling. Experimental parameters resulting in systematic biases in gene expression were also uncovered. In particular, we found that the late competence operons comE, comF and comG were associated with subtle variations in growth conditions.

Conclusions

Using variance analysis it is possible to distinguish between systematic biases and relevant gene-expression variation in transcriptome experiments. Co-variation of metabolic gene expression pathways was thus uncovered linking nitrogen and sulfur metabolism in B. subtilis.