Energy metabolism in Desulfovibrio vulgaris Hildenborough: insights from transcriptome analysis

Pereira, Patrícia M.; He, Qiang; Valente, Filipa M. A.; Xavier, António V.; Zhou, Jizhong; Pereira, Inês; Louro, Ricardo O.

doi:10.1007/s10482-007-9212-0

Cited by 71 publications

(91 citation statements)

References 49 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The g value (2.003) and strong hyperfine coupling to a single proton (1.3 mT) indicate the presence of an organic radical located at the α-carbon of an amino acid and are consistent with previously reported EPR spectra of cells expressing glycyl radical enzymes (30,31). The weaker nonhyperfine isotropic signal observed for cells from pyruvate cultures likely originates from flavoproteins, which are produced by a related Desulfovibrio strain during growth on pyruvate (32). Overall, these EPR experiments link choline utilization to a glycine-centered radical and indicate that choline TMA-lyase CutC is a member of the glycyl radical enzyme family.…”

Section: Resultssupporting

confidence: 88%

Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme

Craciun

Balskus

2012

Proc. Natl. Acad. Sci. U.S.A.

583

578

View full text Add to dashboard Cite

Choline and trimethylamine (TMA) are small molecules that play central roles in biological processes throughout all kingdoms of life. These ubiquitous metabolites are linked through a single biochemical transformation, the conversion of choline to TMA by anaerobic microorganisms. This metabolic activity, which contributes to methanogenesis and human disease, has been known for over a century but has eluded genetic and biochemical characterization. We have identified a gene cluster responsible for anaerobic choline degradation within the genome of a sulfate-reducing bacterium and verified its function using both a genetic knockout strategy and heterologous expression in Escherichia coli. Bioinformatics and electron paramagnetic resonance (EPR) spectroscopy revealed the involvement of a C-N bond cleaving glycyl radical enzyme in TMA production, which is unprecedented chemistry for this enzyme family. Our discovery provides the predictive capabilities needed to identify choline utilization clusters in numerous bacterial genomes, underscoring the importance and prevalence of this metabolic activity within the human microbiota and the environment.fragmentation | choline trimethylamine-lyase | gastrointestinal tract | metabolism | trimethylaminuria

show abstract

Section: Resultssupporting

confidence: 88%

Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme

Craciun

Balskus

2012

Proc. Natl. Acad. Sci. U.S.A.

583

578

View full text Add to dashboard Cite

show abstract

“…In addition, a formate dehydrogenase gene cluster (DVU0586-0588) had increased expression under nitrate stress (data not shown). The composite of these differentially expressed genes appears to be consistent with an increased flow of reducing equivalent cycling through formate as a metabolic intermediate, as suggested under certain growth conditions Pereira et al, 2008).…”

Section: Genes Involved In Energy Metabolismsupporting

confidence: 70%

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

Joyner

et al. 2010

The ISME Journal

Self Cite

View full text Add to dashboard Cite

Sulfate-reducing bacteria have been extensively studied for their potential in heavy-metal bioremediation. However, the occurrence of elevated nitrate in contaminated environments has been shown to inhibit sulfate reduction activity. Although the inhibition has been suggested to result from the competition with nitrate-reducing bacteria, the possibility of direct inhibition of sulfate reducers by elevated nitrate needs to be explored. Using Desulfovibrio vulgaris as a model sulfate-reducing bacterium, functional genomics analysis reveals that osmotic stress contributed to growth inhibition by nitrate as shown by the upregulation of the glycine/betaine transporter genes and the relief of nitrate inhibition by osmoprotectants. The observation that significant growth inhibition was effected by 70 mM NaNO 3 but not by 70 mM NaCl suggests the presence of inhibitory mechanisms in addition to osmotic stress. The differential expression of genes characteristic of nitrite stress responses, such as the hybrid cluster protein gene, under nitrate stress condition further indicates that nitrate stress response by D. vulgaris was linked to components of both osmotic and nitrite stress responses. The involvement of the oxidative stress response pathway, however, might be the result of a more general stress response. Given the low similarities between the response profiles to nitrate and other stresses, less-defined stress response pathways could also be important in nitrate stress, which might involve the shift in energy metabolism. The involvement of nitrite stress response upon exposure to nitrate may provide detoxification mechanisms for nitrite, which is inhibitory to sulfate-reducing bacteria, produced by microbial nitrate reduction as a metabolic intermediate and may enhance the survival of sulfate-reducing bacteria in environments with elevated nitrate level.

show abstract

“…Thus, although the core metabolic machinery for sulphate reduction is conserved in all studied SRMs, there is a substantial variation in the mechanisms of redox cycling and electron flow, and novel mechanisms of energy conservation may remain to be discovered. Indeed, the plethora of redox proteins that are involved in energy metabolism in D. vulgaris H. exhibit complex gene expression patterns that are specific to distinct stress conditions, demonstrating the importance of adjustments in energy metabolism pathways as a central strategy in the stress response [37][38][39][40][41] . Even less is known about sulphate reduction and electron transport in sulphate-reducing Nitrospira spp.…”

mentioning

confidence: 99%

How sulphate-reducing microorganisms cope with stress: lessons from systems biology

et al. 2011

Self Cite

View full text Add to dashboard Cite

| Sulphate-reducing microorganisms (SRMs) are a phylogenetically diverse group of anaerobes encompassing distinct physiologies with a broad ecological distribution. As SRMs have important roles in the biogeochemical cycling of carbon, nitrogen, sulphur and various metals, an understanding of how these organisms respond to environmental stresses is of fundamental and practical importance. In this Review, we highlight recent applications of systems biology tools in studying the stress responses of SRMs, particularly Desulfovibrio spp., at the cell, population, community and ecosystem levels. The syntrophic lifestyle of SRMs is also discussed, with a focus on system-level analyses of adaptive mechanisms. Such information is important for understanding the microbiology of the global sulphur cycle and for developing biotechnological applications of SRMs for environmental remediation, energy production, biocorrosion control, wastewater treatment and mineral recovery.

show abstract

Energy metabolism in Desulfovibrio vulgaris Hildenborough: insights from transcriptome analysis

Cited by 71 publications

References 49 publications

Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme

Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme

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

How sulphate-reducing microorganisms cope with stress: lessons from systems biology

Contact Info

Product

Resources

About