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

Abstract

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.The sulfate-reducing bacteria represent a group of microorganisms characterized by the ability to use sulfate as an electron acceptor in anaerobic respiration (47). Microbial sulfate reduction by these microorganisms is recognized as a widely distributed process of great ecological importance (29,54). Historical interest in sulfate-reducing bacteria has been focused on their involvement in biocorrosion of ferrous metals in the petroleum industry and of concrete structures in wastewater collection systems (15,24). More recent studies (7, 25, 27, 28) have documented the ability of a number of sulfate-reducing bacteria to reduce soluble metal oxyanions to insoluble forms, a process of great potential in the bioremediation of toxic heavy metals and radionuclides such as chromium and uranium (11, 56).To effectively immobilize heavy metals and radionuclides using sulfate-reducing bacteria, it is important to understand the microbial response to adverse environmental factors common in contaminated subsurface environments. One such factor is the high nitrate concentration of many contaminated sites at the nuclear weapon complexes in the United States managed by the Department of Energy (39,49). The presence of nitrate may pose a specific stress to sulfate-reducing bacteria as nitrate has been observed to suppress sulfate reduction activity in situ (9, 21). However, it has been suggested that nitrite, an intermediate that transiently accumulates during nitrate reduction (3,23,58), is directly...

Impact of elevated nitrate on sulfate-reducing bacteria: a comparative Study of Desulfovibrio vulgaris

“…It is noted that this gene was among the most highly up-regulated (log 2 R ¼ 6.4) under nitrite stress He et al, 2006). The iron-sulfur cluster-binding protein, predicted to be encoded promoter distal in the same operon (DVU2544), was also increased in expression (log 2 R ¼ 1.9), representing a shared response to nitrate and nitrite stress (Table 1).…”

“…The accuracy of the microarrays in global transcriptional profiling has been extensively tested and validated in previous studies on stress response pathways in D. vulgaris (Clark et al, 2006;He et al, 2006). All microarray procedures including the extraction and labeling of nucleic acids, microarray hybridization and washing, and data analysis were performed using previously published protocols .…”

Functional Characterization of Crp/Fnr-Type Global Transcriptional Regulators in Desulfovibrio vulgaris Hildenborough

“…Most of the data sets have been published and deposited in the NCBI GEO database as follows: nitrate stress (accession no. GSE20079), nitrite stress (16), air stress (GSE8196), H 2 O 2 stress (GSE21441), ethanol stress (GSE7489), heat shock stress (7), and salt adaptation stress (GSE14343).…”

“…Isolation, fluorophore dye labeling, and handling of total RNA or gDNA were performed as described previously (48). DNA microarrays used in this study covered 3,482 of the 3,531 annotated protein-coding sequences of the D. vulgaris genome (16). Each array was hybridized with Cy3-labeled gDNA (as a control for normalization) and Cy5-labeled cDNA on a Tecan HS4800 hybridization station (Tecan Group, Durham, NC).…”

“…Each array was hybridized with Cy3-labeled gDNA (as a control for normalization) and Cy5-labeled cDNA on a Tecan HS4800 hybridization station (Tecan Group, Durham, NC). Hybridization conditions as well as washing conditions and performance of image scanning were as described previously (7,16,36,51). The microarray raw data processing was performed as described previously (36).…”