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Open Access Research article

Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis

Martin Follmann1, Ines Ochrombel1, Reinhard Krämer1, Christian Trötschel2, Ansgar Poetsch2, Christian Rückert3, Andrea Hüser3, Marcus Persicke4, Dominic Seiferling1, Jörn Kalinowski3 and Kay Marin1*

Author Affiliations

1 University of Cologne, Institute of Biochemistry, Zuelpicher Str. 47, 50674 Cologne, Germany

2 Ruhr-University of Bochum, Plant Biochemistry, Universitaetsstrasse 150, 44801 Bochum, Germany

3 Institute for Genome Research and Systems Biology at the Centre for Biotechnology (CeBiTec), Universitaetsstr. 27, 33615, Bielefeld, Gemany

4 University of Bielefeld, Department of Genetics, Universitaetsstr. 25, 33615, Bielefeld, Germany

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BMC Genomics 2009, 10:621  doi:10.1186/1471-2164-10-621

Published: 21 December 2009

Abstract

Background

The maintenance of internal pH in bacterial cells is challenged by natural stress conditions, during host infection or in biotechnological production processes. Comprehensive transcriptomic and proteomic analyses has been conducted in several bacterial model systems, yet questions remain as to the mechanisms of pH homeostasis.

Results

Here we present the comprehensive analysis of pH homeostasis in C. glutamicum, a bacterium of industrial importance. At pH values between 6 and 9 effective maintenance of the internal pH at 7.5 ± 0.5 pH units was found. By DNA microarray analyses differential mRNA patterns were identified. The expression profiles were validated and extended by 1D-LC-ESI-MS/MS based quantification of soluble and membrane proteins. Regulators involved were identified and thereby participation of numerous signaling modules in pH response was found. The functional analysis revealed for the first time the occurrence of oxidative stress in C. glutamicum cells at neutral and low pH conditions accompanied by activation of the iron starvation response. Intracellular metabolite pool analysis unraveled inhibition of the TCA and other pathways at low pH. Methionine and cysteine synthesis were found to be activated via the McbR regulator, cysteine accumulation was observed and addition of cysteine was shown to be toxic under acidic conditions.

Conclusions

Novel limitations for C. glutamicum at non-optimal pH values were identified by a comprehensive analysis on the level of the transcriptome, proteome, and metabolome indicating a functional link between pH acclimatization, oxidative stress, iron homeostasis, and metabolic alterations. The results offer new insights into bacterial stress physiology and new starting points for bacterial strain design or pathogen defense.