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Applied and Environmental Microbiology, June 2006, p. 4370-4381, Vol. 72, No. 6
0099-2240/06/$08.00+0     doi:10.1128/AEM.02609-05
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Energetic Consequences of Nitrite Stress in Desulfovibrio vulgaris Hildenborough, Inferred from Global Transcriptional Analysis

Virtual Institute for Microbial Stress and Survival, Berkeley, California 94720^,, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,² Department of Civil and Environmental Engineering, Temple University, Philadelphia, Pennsylvania 19122,³ Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720,⁴ Department of Microbiology, Miami University, Oxford, Ohio 45056,⁵ Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720,⁶ Department of Bioengineering, University of California, Berkeley, California 94720,⁷ Howard Hughes Medical Institute, Chevy Chase, Maryland 20815,⁸ Departments of Biochemistry and Molecular Microbiology and Immunology, University of Missouri—Columbia, Columbia, Missouri 65211,⁹ Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019,¹⁰

Received 4 November 2005/ Accepted 18 March 2006

Many of the proteins that are candidates for bioenergetic pathways involved with sulfate respiration in Desulfovibrio spp. have been studied, but complete pathways and overall cell physiology remain to be resolved for many environmentally relevant conditions. In order to understand the metabolism of these microorganisms under adverse environmental conditions for improved bioremediation efforts, Desulfovibrio vulgaris Hildenborough was used as a model organism to study stress response to nitrite, an important intermediate in the nitrogen cycle. Previous physiological studies demonstrated that growth was inhibited by nitrite and that nitrite reduction was observed to be the primary mechanism of detoxification. Global transcriptional profiling with whole-genome microarrays revealed coordinated cascades of responses to nitrite in pathways of energy metabolism, nitrogen metabolism, oxidative stress response, and iron homeostasis. In agreement with previous observations, nitrite-stressed cells showed a decrease in the expression of genes encoding sulfate reduction functions in addition to respiratory oxidative phosphorylation and ATP synthase activity. Consequently, the stressed cells had decreased expression of the genes encoding ATP-dependent amino acid transporters and proteins involved in translation. Other genes up-regulated in response to nitrite include the genes in the Fur regulon, which is suggested to be involved in iron homeostasis, and genes in the Per regulon, which is predicted to be responsible for oxidative stress response.

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