Characterization of sulfate-reducing bacteria isolated from Senegal ricefields

Ouattara, Aboubakar S.; Jacq, Vincent

doi:10.1111/j.1574-6941.1992.tb01658.x

Cited by 22 publications

(21 citation statements)

References 25 publications

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“…Analysis of the genome of the model sulfate-reducing bacterium (SRB) Desulfovibrio vulgaris Hildenborough revealed four annotated Crp/Fnr-type regulators (DVU0379, DVU2097, DVU2547, and DVU3111), suggesting potential functional differentiations among the multiple Crp/Fnr-type regulators, which exhibit a remarkable ability to survive and adapt to environmental perturbations and stress conditions (32,40,46,52 Therefore, the objectives of this study were to (i) examine the activities of the four fnr/crp-type regulatory genes in the control of stress responses and (ii) identify the potential specificity of each Crp/Fnr-type regulator for various stress conditions in D. vulgaris. To address these objectives, knockout mutants for each Crp/Fnr regulator were generated and functionally characterized by their response to various environmental stress conditions that included air, NaCl, nitrite, and Cr(VI) by growth phenotype, transcriptional profiling, and competition analysis.…”

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

Zhou

Chen

Zane

et al. 2012

Appl Environ Microbiol

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Crp/Fnr-type global transcriptional regulators regulate various metabolic pathways in bacteria and typically function in response to environmental changes. However, little is known about the function of four annotated Crp/Fnr homologs (DVU0379, DVU2097, DVU2547, and DVU3111) in Desulfovibrio vulgaris Hildenborough. A systematic study using bioinformatic, transcriptomic, genetic, and physiological approaches was conducted to characterize their roles in stress responses. Similar growth phenotypes were observed for the crp/fnr deletion mutants under multiple stress conditions. Nevertheless, the idea of distinct functions of Crp/Fnr-type regulators in stress responses was supported by phylogeny, gene transcription changes, fitness changes, and physiological differences. The four D. vulgaris Crp/Fnr homologs are localized in three subfamilies (HcpR, CooA, and cc). The crp/fnr knockout mutants were well separated by transcriptional profiling using detrended correspondence analysis (DCA), and more genes significantly changed in expression in a ⌬DVU3111 mutant (JW9013) than in the other three paralogs. In fitness studies, strain JW9013 showed the lowest fitness under standard growth conditions (i.e., sulfate reduction) and the highest fitness under NaCl or chromate stress conditions; better fitness was observed for a ⌬DVU2547 mutant (JW9011) under nitrite stress conditions and a ⌬DVU2097 mutant (JW9009) under air stress conditions. A higher Cr(VI) reduction rate was observed for strain JW9013 in experiments with washed cells. These results suggested that the four Crp/Fnr-type global regulators play distinct roles in stress responses of D. vulgaris. DVU3111 is implicated in responses to NaCl and chromate stresses, DVU2547 in nitrite stress responses, and DVU2097 in air stress responses.T ranscription factors, promoter sequences, and regulatory circuit architecture are often referred as "the regulatory genome" (27, 33), and transcription factors are central to the function of regulatory networks (5). Organisms rely on regulatory networks to orchestrate the transcription of genes in response to internal or external environmental changes in order to optimize metabolism and enhance survival. Crp/Fnr regulators are global transcriptional regulators widely distributed in bacteria. The characteristic structure of Crp/Fnr is a C-terminal helix-turn-helix (HTH) motif that fits the DNA major groove and an N-terminal nucleotide binding domain (34). This class of transcriptional factors is named after the first two representatives discovered in Escherichia coli, i.e., the Crp (cyclic AMP [cAMP] receptor protein) and Fnr (fumarate and nitrate reductase regulator protein) (4, 21, 24, 27). Crp/Fnr regulators are generally classified into different subfamilies (e.g., CooA, Crp, Dnr, FixK, Fnr, HbaR, NnrR, etc.) according to phylogenetic affiliations (50). The increasing number of sequenced whole genomes has added to a growing list of Crp/Fnr family regulators identified in bacteria (9, 26); however, functions for most are not well defin...

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

Zhou

Chen

Zane

et al. 2012

Appl Environ Microbiol

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“…Originally isolated in 1946 from clay soils in Hildenborough, Kent, United Kingdom, Desulfovibrio vulgaris Hildenborough belongs to the sulfate-reducing class of bacteria that are ubiquitous in nature (23,45). These anaerobes generate energy by reducing sulfate (42) and play important roles in global sulfur cycling and complete mineralization of organic matter.…”

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Salt Stress in Desulfovibrio vulgaris Hildenborough: an Integrated Genomics Approach

et al. 2006

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The ability of Desulfovibrio vulgaris Hildenborough to reduce, and therefore contain, toxic and radioactive metal waste has made all factors that affect the physiology of this organism of great interest. Increased salinity is an important and frequent fluctuation faced by D. vulgaris in its natural habitat. In liquid culture, exposure to excess salt resulted in striking elongation of D. vulgaris cells. Using data from transcriptomics, proteomics, metabolite assays, phospholipid fatty acid profiling, and electron microscopy, we used a systems approach to explore the effects of excess NaCl on D. vulgaris. In this study we demonstrated that import of osmoprotectants, such as glycine betaine and ectoine, is the primary mechanism used by D. vulgaris to counter hyperionic stress. Several efflux systems were also highly up-regulated, as was the ATP synthesis pathway. Increases in the levels of both RNA and DNA helicases suggested that salt stress affected the stability of nucleic acid base pairing. An overall increase in the level of branched fatty acids indicated that there were changes in cell wall fluidity. The immediate response to salt stress included up-regulation of chemotaxis genes, although flagellar biosynthesis was down-regulated. Other down-regulated systems included lactate uptake permeases and ABC transport systems. The results of an extensive NaCl stress analysis were compared with microarray data from a KCl stress analysis, and unlike many other bacteria, D. vulgaris responded similarly to the two stresses. Integration of data from multiple methods allowed us to develop a conceptual model for the salt stress response in D. vulgaris that can be compared to those in other microorganisms.Originally isolated in 1946 from clay soils in Hildenborough, Kent, United Kingdom, Desulfovibrio vulgaris Hildenborough belongs to the sulfate-reducing class of bacteria that are ubiquitous in nature (23, 45). These anaerobes generate energy by reducing sulfate (42) and play important roles in global sulfur cycling and complete mineralization of organic matter. D. vulgaris has been implicated in biocorrosion of oil and gas pipelines both on land and in the ocean (5, 23, 57). Members of this species have also been found to reduce metals in sediments and soils with high concentrations of NaCl and a milieu of toxic metals (6) and to cope with salt stresses that result from environmental hydration-dehydration cycles. An understanding of the ability of D. vulgaris to survive in the presence of high concentrations of NaCl and osmotic stress is critical for determining the biogeochemistry at metal-contaminated sites for bioremediation and natural attenuation and for predicting the potential for biocorrosion of pipelines and tanks in soils, sediments, and off-shore oil production facilities (8,38,62). The availability of an annotated genomic sequence for D. vulgaris makes this organism ideal for studying the complex physiology of sulfate-reducing bacteria (25).The bacterial response to hyperionic stress includes a range of mechan...

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“…FT-ICR MS was used to locate the labeled carbon distribution in aspartate and glutamate and confirmed the presence of an atypical enzyme for citrate formation suggested in previous reports [the citrate synthesized by this enzyme is the isotopic antipode of the citrate synthesized by the (S)-citrate synthase]. These findings enable a better understanding of the relation between genome annotation and actual metabolic pathways in D. vulgaris and also demonstrate that FT-ICR MS is a powerful tool for isotopomer analysis, overcoming the problems with both GC-MS and nuclear magnetic resonance spectroscopy.Sulfate-reducing bacteria (SRB) such as Desulfovibrio vulgaris Hildenborough are ubiquitous in nature and play an important role in global sulfur cycling and the mineralization of organic matter (21,38,39). The uncontrolled growth of D. vulgaris contributes to the biocorrosion of oil and gas pipelines and the souring of production wells (18,37,53).…”

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“…Sulfate-reducing bacteria (SRB) such as Desulfovibrio vulgaris Hildenborough are ubiquitous in nature and play an important role in global sulfur cycling and the mineralization of organic matter (21,38,39). The uncontrolled growth of D. vulgaris contributes to the biocorrosion of oil and gas pipelines and the souring of production wells (18,37,53).…”

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Pathway Confirmation and Flux Analysis of Central Metabolic Pathways in Desulfovibrio vulgaris Hildenborough using Gas Chromatography-Mass Spectrometry and Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry

et al. 2007

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Flux distribution in central metabolic pathways of Desulfovibrio vulgaris Hildenborough was examined using 13 C tracer experiments. Consistent with the current genome annotation and independent evidence from enzyme activity assays, the isotopomer results from both gas chromatography-mass spectrometry (GC-MS) and Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) indicate the lack of an oxidatively functional tricarboxylic acid (TCA) cycle and an incomplete pentose phosphate pathway. Results from this study suggest that fluxes through both pathways are limited to biosynthesis. The data also indicate that >80% of the lactate was converted to acetate and that the reactions involved are the primary route of energy production [NAD(P)H and ATP production]. Independently of the TCA cycle, direct cleavage of acetyl coenzyme A to CO and 5,10-methyl tetrahydrofuran also leads to production of NADH and ATP. Although the genome annotation implicates a ferredoxin-dependent oxoglutarate synthase, isotopic evidence does not support flux through this reaction in either the oxidative or the reductive mode; therefore, the TCA cycle is incomplete. FT-ICR MS was used to locate the labeled carbon distribution in aspartate and glutamate and confirmed the presence of an atypical enzyme for citrate formation suggested in previous reports [the citrate synthesized by this enzyme is the isotopic antipode of the citrate synthesized by the (S)-citrate synthase]. These findings enable a better understanding of the relation between genome annotation and actual metabolic pathways in D. vulgaris and also demonstrate that FT-ICR MS is a powerful tool for isotopomer analysis, overcoming the problems with both GC-MS and nuclear magnetic resonance spectroscopy.Sulfate-reducing bacteria (SRB) such as Desulfovibrio vulgaris Hildenborough are ubiquitous in nature and play an important role in global sulfur cycling and the mineralization of organic matter (21,38,39). The uncontrolled growth of D. vulgaris contributes to the biocorrosion of oil and gas pipelines and the souring of production wells (18,37,53). Conversely, the ability of D. vulgaris to reduce heavy metals and radionuclides to insoluble forms provides a unique microbe-oriented solution for bioremediation (25,27,28). In addition to its environmental importance, D. vulgaris has a unique energy metabolism that has the potential to be used for hydrogen or methane production in either pure or mixed cultures (7,13,38,49).The availability of an annotated genome sequence for D. vulgaris (25) makes it an ideal organism for investigating SRB physiology, and several functional genomics studies have described the transcriptome and proteome of this organism (10,24,35). Information from these analyses is critical for validating genome annotation and predictions for operons and regulons. Moreover, D. vulgaris metabolism has been studied for several decades, but the recently published annotated genomic sequence of D. vulgaris contained the following unresolved predictions related to k...

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Characterization of sulfate-reducing bacteria isolated from Senegal ricefields

Cited by 22 publications

References 25 publications

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

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

Salt Stress in Desulfovibrio vulgaris Hildenborough: an Integrated Genomics Approach

Pathway Confirmation and Flux Analysis of Central Metabolic Pathways in Desulfovibrio vulgaris Hildenborough using Gas Chromatography-Mass Spectrometry and Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry

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