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Environmental Microbiology May 2018Syntrophobacter fumaroxidans is a sulfate-reducing bacterium able to grow on propionate axenically or in syntrophic interaction with methanogens or other...
Syntrophobacter fumaroxidans is a sulfate-reducing bacterium able to grow on propionate axenically or in syntrophic interaction with methanogens or other sulfate-reducing bacteria. We performed a proteome analysis of S. fumaroxidans growing with propionate axenically with sulfate or fumarate, and in syntrophy with Methanospirillum hungatei, Methanobacterium formicicum or Desulfovibrio desulfuricans. Special attention was put on the role of hydrogen and formate in interspecies electron transfer (IET) and energy conservation. Formate dehydrogenase Fdh1 and hydrogenase Hox were the main confurcating enzymes used for energy conservation. In the periplasm, Fdh2 and hydrogenase Hyn play an important role in reverse electron transport associated with succinate oxidation. Periplasmic Fdh3 and Fdh5 were involved in IET. The sulfate reduction pathway was poorly regulated and many enzymes associated with sulfate reduction (Sat, HppA, AprAB, DsrAB and DsrC) were abundant even at conditions where sulfate was not present. Proteins similar to heterodisulfide reductases (Hdr) were abundant. Hdr/Flox was detected in all conditions while HdrABC/HdrL was exclusively detected when sulfate was available; these complexes most likely confurcate electrons. Our results suggest that S. fumaroxidans mainly used formate for electron release and that different confurcating mechanisms were used in its sulfidogenic metabolism.
Topics: Coculture Techniques; Deltaproteobacteria; Desulfovibrio; Electron Transport; Formate Dehydrogenases; Formates; Hydrogen; Hydrogenase; Methanobacterium; Methanospirillum; Oxidation-Reduction; Propionates; Proteome; Sulfates
PubMed: 29611893
DOI: 10.1111/1462-2920.14119 -
Frontiers in Microbiology 2020Microorganisms are key players in the transformation of mercury into neurotoxic methylmercury (MeHg). Nevertheless, this mechanism and the opposite MeHg demethylation...
Microorganisms are key players in the transformation of mercury into neurotoxic methylmercury (MeHg). Nevertheless, this mechanism and the opposite MeHg demethylation remain poorly understood. Here, we explored the impact of inorganic mercury (IHg) and MeHg concentrations from 0.05 to 50 μM on the production and degradation of MeHg in two sulfate-reducing bacteria, BerOc1 able to methylate and demethylate mercury and G200 only able to demethylate MeHg. MeHg produced by BerOc1 increased with increasing IHg concentration with a maximum attained for 5 μM, and suggested a saturation of the process. MeHg was mainly found in the supernatant suggesting its export from the cell. Hg L-edge High- Energy-Resolution-Fluorescence-Detected-X-ray-Absorption-Near-Edge-Structure spectroscopy (HERFD-XANES) identified MeHg produced by BerOc1 as MeHg-cysteine form. A dominant tetracoordinated βHgS form was detected for BerOc1 exposed to the lowest IHg concentrations where methylation was detected. In contrast, at the highest exposure (50 μM) where Hg methylation was abolished, Hg species drastically changed suggesting a role of Hg speciation in the production of MeHg. The tetracoordinated βHgS was likely present as nano-particles as suggested by transmission electron microscopy combined to X-ray energy dispersive spectroscopy (TEM-X-EDS) and nano-X ray fluorescence (nano-XRF). When exposed to MeHg, the production of IHg, on the contrary, increased with the increase of MeHg exposure until 50 μM for both BerOc1 and G200 strains, suggesting that demethylation did not require intact biological activity. The formed IHg species were identified as various tetracoordinated Hg-S forms. These results highlight the important role of thiol ligands and Hg coordination in Hg methylation and demethylation processes.
PubMed: 33154741
DOI: 10.3389/fmicb.2020.584715 -
MicrobiologyOpen Aug 2014Desulfovibrio gigas is a model organism of sulfate-reducing bacteria of which energy metabolism and stress response have been extensively studied. The complete genomic... (Comparative Study)
Comparative Study
Desulfovibrio gigas is a model organism of sulfate-reducing bacteria of which energy metabolism and stress response have been extensively studied. The complete genomic context of this organism was however, not yet available. The sequencing of the D. gigas genome provides insights into the integrated network of energy conserving complexes and structures present in this bacterium. Comparison with genomes of other Desulfovibrio spp. reveals the presence of two different CRISPR/Cas systems in D. gigas. Phylogenetic analysis using conserved protein sequences (encoded by rpoB and gyrB) indicates two main groups of Desulfovibrio spp, being D. gigas more closely related to D. vulgaris and D. desulfuricans strains. Gene duplications were found such as those encoding fumarate reductase, formate dehydrogenase, and superoxide dismutase. Complexes not yet described within Desulfovibrio genus were identified: Mnh complex, a v-type ATP-synthase as well as genes encoding the MinCDE system that could be responsible for the larger size of D. gigas when compared to other members of the genus. A low number of hydrogenases and the absence of the codh/acs and pfl genes, both present in D. vulgaris strains, indicate that intermediate cycling mechanisms may contribute substantially less to the energy gain in D. gigas compared to other Desulfovibrio spp. This might be compensated by the presence of other unique genomic arrangements of complexes such as the Rnf and the Hdr/Flox, or by the presence of NAD(P)H related complexes, like the Nuo, NfnAB or Mnh.
Topics: Bacterial Proteins; Cluster Analysis; Conserved Sequence; DNA, Bacterial; Desulfovibrio gigas; Genetic Variation; Genome, Bacterial; Molecular Sequence Data; Phylogeny; Sequence Analysis, DNA
PubMed: 25055974
DOI: 10.1002/mbo3.184 -
Angewandte Chemie (International Ed. in... Aug 2018A combination of nuclear resonance vibrational spectroscopy (NRVS), FTIR spectroscopy, and DFT calculations was used to observe and characterize Fe-H/D bending modes in...
A combination of nuclear resonance vibrational spectroscopy (NRVS), FTIR spectroscopy, and DFT calculations was used to observe and characterize Fe-H/D bending modes in CrHydA1 [FeFe]-hydrogenase Cys-to-Ser variant C169S. Mutagenesis of cysteine to serine at position 169 changes the functional group adjacent to the H-cluster from a -SH to -OH, thus altering the proton transfer pathway. The catalytic activity of C169S is significantly reduced compared to that of native CrHydA1, presumably owing to less efficient proton transfer to the H-cluster. This mutation enabled effective capture of a hydride/deuteride intermediate and facilitated direct detection of the Fe-H/D normal modes. We observed a significant shift to higher frequency in an Fe-H bending mode of the C169S variant, as compared to previous findings with reconstituted native and oxadithiolate (ODT)-substituted CrHydA1. On the basis of DFT calculations, we propose that this shift is caused by the stronger interaction of the -OH group of C169S with the bridgehead -NH- moiety of the active site, as compared to that of the -SH group of C169 in the native enzyme.
Topics: Catalytic Domain; Clostridium; Density Functional Theory; Desulfovibrio desulfuricans; Hydrogenase; Iron; Mutagenesis, Site-Directed; Protons; Spectroscopy, Fourier Transform Infrared
PubMed: 29923293
DOI: 10.1002/anie.201805144 -
Environmental Science & Technology Jul 2020To advance the scientific understanding of bacteria-driven mercury (Hg) transformation processes in natural environments, thermodynamics and kinetics of divalent mercury...
To advance the scientific understanding of bacteria-driven mercury (Hg) transformation processes in natural environments, thermodynamics and kinetics of divalent mercury Hg(II) chemical speciation need to be understood. Based on Hg L-edge extended X-ray absorption fine structure (EXAFS) spectroscopic information, combined with competitive ligand exchange (CLE) experiments, we determined Hg(II) structures and thermodynamic constants for Hg(II) complexes formed with thiol functional groups in bacterial cell membranes of two extensively studied Hg(II) methylating bacteria: PCA and ND132. The Hg EXAFS data suggest that 5% of the total number of membranethiol functionalities (Mem-RS = 380 ± 50 μmol g C) are situated closely enough to be involved in a 2-coordinated Hg(Mem-RS) structure in . The remaining 95% of Mem-RSH is involved in mixed-ligation Hg(II)-complexes, combining either with low molecular mass (LMM) thiols like Cys, Hg(Cys)(Mem-RS), or with neighboring O/N membrane functionalities, Hg(Mem-RSRO). We report log values for the formation of the structures Hg(Mem-RS), Hg(Cys)(Mem-RS), and Hg(Mem-RSRO) to be 39.1 ± 0.2, 38.1 ± 0.1, and 25.6 ± 0.1, respectively, for and 39.2 ± 0.2, 38.2 ± 0.1, and 25.7 ± 0.1, respectively, for ND132. Combined with results obtained from previous studies using the same methodology to determine chemical speciation of Hg(II) in the presence of natural organic matter (NOM; Suwannee River DOM) and 15 LMM thiols, an internally consistent thermodynamic data set is created, which we recommend to be used in studies of Hg transformation processes in bacterium-NOM-LMM thiol systems.
Topics: Geobacter; Mercury; Rivers; Sulfhydryl Compounds
PubMed: 32491838
DOI: 10.1021/acs.est.0c01751 -
Food Science & Nutrition Dec 2020Studies have documented the benefits of fish oil in different diseases because of its high n-3 polyunsaturated fatty acid content. However, these studies mostly used...
Studies have documented the benefits of fish oil in different diseases because of its high n-3 polyunsaturated fatty acid content. However, these studies mostly used commercially available fish oil supplements with a ratio of 18/12 for eicosapentaenoic acid and docosahexaenoic acid (DHA). However, increasing DHA content for this commonly used ratio might bring out a varied metabolic effect, which have remained unclear. Thus, in this study, a novel tuna oil (TO) was applied to investigate the effect of high-DHA content on the alteration of the gut microbiota and obesity in high-fat diet mice. The results suggest that high-DHA TO (HDTO) supplementation notably ameliorates obesity and related lipid parameters and restores the expression of lipid metabolism-related genes. The benefits of TOs were derived from their modification of the gut microbiota composition and structure in mice. A high-fat diet triggered an increased / ratio that was remarkably restored by TOs. The number of obesity-promoting bacteria-, , , , , , and was dramatically reduced. , , and , three dysbiosis-related species, were especially regulated by HDTO. Regarding the prevention of obesity, HDTO outperforms the normal TO. Intriguingly, HDTO feeding to HFD-fed mice might alter the arginine and proline metabolism of intestinal microbiota.
PubMed: 33312536
DOI: 10.1002/fsn3.1941 -
Diseases of Aquatic Organisms Feb 2016The etiology of black band disease (BBD), a persistent, globally distributed coral disease characterized by a dark microbial mat, is still unclear. A metatranscriptomics...
The etiology of black band disease (BBD), a persistent, globally distributed coral disease characterized by a dark microbial mat, is still unclear. A metatranscriptomics approach was used to unravel the roles of the major mat constituents in the disease process. By comparing the transcriptomes of the mat constituents with those of the surface microbiota of diseased and healthy corals, we showed a shift in bacterial composition and function in BBD-affected corals. mRNA reads of Cyanobacteria, Bacteroidetes and Firmicutes phyla were prominent in the BBD mat. Cyanobacterial adenosylhomocysteinase, involved in cyanotoxin production, was the most transcribed gene in the band consortium. Pathogenic and non-pathogenic forms of Vibrio spp., mainly transcribing the thiamine ABC transporter, were abundant and highly active in both the band and surface tissues. Desulfovibrio desulfuricans was the primary producer of sulfide in the band. Members of the Bacilli class expressed high levels of rhodanese, an enzyme responsible for cyanide and sulfide detoxification. These results offer a first look at the varied functions of the microbiota in the disease mat and surrounding coral surface and enabled us to develop an improved functional model for this disease.
Topics: Animals; Anthozoa; Cyanobacteria; Host-Pathogen Interactions; Seasons; Transcriptome
PubMed: 26865237
DOI: 10.3354/dao02952 -
Revista Espanola de Quimioterapia :... Feb 2024
Topics: Humans; Abscess; Desulfovibrio desulfuricans; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Anti-Bacterial Agents; Actinobacteria
PubMed: 38050695
DOI: 10.37201/req/081.2023 -
Applied and Environmental Microbiology May 2015Methylmercury is a potent neurotoxin that is produced by anaerobic microorganisms from inorganic mercury by a recently discovered pathway. A two-gene cluster, consisting...
Methylmercury is a potent neurotoxin that is produced by anaerobic microorganisms from inorganic mercury by a recently discovered pathway. A two-gene cluster, consisting of hgcA and hgcB, encodes two of the proteins essential for this activity. hgcA encodes a corrinoid protein with a strictly conserved cysteine proposed to be the ligand for cobalt in the corrinoid cofactor, whereas hgcB encodes a ferredoxin-like protein thought to be an electron donor to HgcA. Deletion of either gene eliminates mercury methylation by the methylator Desulfovibrio desulfuricans ND132. Here, site-directed mutants of HgcA and HgcB were constructed to determine amino acid residues essential for mercury methylation. Mutations of the strictly conserved residue Cys93 in HgcA, the proposed ligand for the corrinoid cobalt, to Ala or Thr completely abolished the methylation capacity, but a His substitution produced measurable methylmercury. Mutations of conserved amino acids near Cys93 had various impacts on the methylation capacity but showed that the structure of the putative "cap helix" region harboring Cys93 is crucial for methylation function. In the ferredoxin-like protein HgcB, only one of two conserved cysteines found at the C terminus was necessary for methylation, but either cysteine sufficed. An additional, strictly conserved cysteine, Cys73, was also determined to be essential for methylation. This study supports the previously predicted importance of Cys93 in HgcA for methylation of mercury and reveals additional residues in HgcA and HgcB that facilitate the production of this neurotoxin.
Topics: Amino Acids; Bacterial Proteins; Conserved Sequence; DNA Mutational Analysis; Desulfovibrio desulfuricans; Mercury; Methylmercury Compounds; Mutagenesis, Site-Directed; Mutant Proteins
PubMed: 25724962
DOI: 10.1128/AEM.00217-15 -
Journal of the American Chemical Society Nov 2017[FeFe]-hydrogenases are metalloenzymes that reversibly reduce protons to molecular hydrogen at exceptionally high rates. We have characterized the catalytically...
[FeFe]-hydrogenases are metalloenzymes that reversibly reduce protons to molecular hydrogen at exceptionally high rates. We have characterized the catalytically competent hydride state (H) in the [FeFe]-hydrogenases from both Chlamydomonas reinhardtii and Desulfovibrio desulfuricans using Fe nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT). H/D exchange identified two Fe-H bending modes originating from the binuclear iron cofactor. DFT calculations show that these spectral features result from an iron-bound terminal hydride, and the Fe-H vibrational frequencies being highly dependent on interactions between the amine base of the catalytic cofactor with both hydride and the conserved cysteine terminating the proton transfer chain to the active site. The results indicate that H is the catalytic state one step prior to H formation. The observed vibrational spectrum, therefore, provides mechanistic insight into the reaction coordinate for H bond formation by [FeFe]-hydrogenases.
Topics: Biocatalysis; Catalytic Domain; Chlamydomonas reinhardtii; Desulfovibrio desulfuricans; Hydrogen; Hydrogenase; Iron; Models, Molecular; Quantum Theory; Spectrum Analysis; Vibration
PubMed: 29054130
DOI: 10.1021/jacs.7b09751