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1.
I J Pickering G N George E Y Yu D C Brune C Tuschak J Overmann J T Beatty R C Prince 《Biochemistry》2001,40(27):8138-8145
Many sulfide-oxidizing organisms, including the photosynthetic sulfur bacteria, store sulfur in "sulfur globules" that are readily detected microscopically. The chemical form of sulfur in these globules is currently the focus of a debate, because they have been described as "liquid" by some observers, although no known allotrope of sulfur is liquid at physiological temperatures. In the present work we have used sulfur K-edge X-ray absorption spectroscopy to identify and quantify the chemical forms of sulfur in a variety of bacterial cells, including photosynthetic sulfur bacteria. We have also taken advantage of X-ray fluorescence self-absorption to derive estimates of the size and density of the sulfur globules in photosynthetic bacteria. We find that the form of sulfur that most resembles the globule sulfur is simply solid S(8), rather than more exotic forms previously proposed. 相似文献
2.
A Prange I Arzberger C Engemann H Modrow O Schumann H G Trüper R Steudel C Dahl J Hormes 《Biochimica et biophysica acta》1999,1428(2-3):446-454
During the oxidation of sulfide and thiosulfate purple and green sulfur bacteria accumulate globules of 'elemental' sulfur. Although essential for a thorough understanding of sulfur metabolism in these organisms, the exact chemical nature of the stored sulfur is still unclear. We applied sulfur K-edge X-ray absorption near edge spectroscopy (XANES) to probe the forms of sulfur in intact cells. Comparing XANES spectra of Allochromatium vinosum, Thiocapsa roseopersicina, Marichromatium purpuratum, Halorhodospira halophila and Chlorobium vibrioforme grown photolithoautotrophically on sulfide with reference probes (fingerprint method), we found sulfur chains with the structure R-S(n)-R. Evidence for the presence of sulfur rings, polythionates and anionic polysulfides in the sulfur globules of these bacteria was not obtained. 相似文献
3.
Huan He Jin-Lan Xia Hong-Chen Jiang Yi Yan Chang-Li Liang Chen-Yan Ma 《Geomicrobiology journal》2013,30(8):707-713
The sulfur chemical speciation in extracellular and intracellular sulfur globules of Acidithiobacillus ferrooxidans and Acidithiobacillus caldus were investigated with an integrated approach including scanning electron microscopy, transmission electron microscopy, energy dispersive spectroscopy and sulfur K-edge X-ray absorption near edge structure spectroscopy (XANES). The results indicated that both strains can accumulate extracellular sulfur globules when grown on thiosulfate, and the major sulfur chemical speciation of which were S8 for A. ferrooxidans and mixture of ring sulfur and polythionate for A. caldus, respectively. In contrast, A. ferrooxidans can accumulate both linear sulfur and S8 internally when grown with sulfur powder and thiosulfate, whereas A. caldus did not accumulate intracellular sulfur globules. In addition, the fitted results of sulfur K-edge XANES spectra indicated that the reduced glutathione (containing thiols groups) were involved in sulfur bio-oxidation of both strains and the tetrathionate were the intermediate products during thiosulfate metabolism by two strains. 相似文献
4.
Density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations have been used to elucidate differences in the sulfur K-edge spectra of three pairs of related compounds: methionine and , cystine and (±)6-thioctic amide, and (Me)2SO3 and (CH2)2SO3. TD-DFT is shown to accurately reproduce all the experimental XAS spectra. The 2 eV energy difference in the sulfur K-edge rising edge position between methionine and trimethylsulfonium is shown to derive from changes in bonding rather than the increase in effective nuclear charge. A similar insensitivity to effective nuclear charge is found in the XAS spectra of cystine and (±)6-thioctic amide. These surprising results are traced back to the fact that XAS spectra reflect orbital energy differences, rather than a measure of the atomic potential. The change in atomic potential following oxidation or reduction affects the core and valence orbitals almost equally. In all cases DFT calculations showed that the dramatic differences in sulfur K-edge spectra found between functional groups in alternative molecular environments derive from the variations in orbital mixing and energies following from bonding. However, XAS rising-edge energy positions have a near linear correlation with oxidation state. This is attributed to the fact that bond strength typically increases with oxidation state. Therefore, although XAS rising-edge energies are an approximate measure of the oxidation state of the absorbing atom, it is important to recognize that the correlation of XAS edge energy with effective nuclear charge is not direct. This result is finally applied to the question of quantitative sulfur speciation in complex materials of chemical, biological, or geological origin. 相似文献
5.
X-ray absorption spectroscopy at the sulfur K-edge (2.4-2.6keV) provides a sensitive and specific technique to identify S-nitroso compounds, which have significance in nitric oxide-based cell signaling. Unique spectral features clearly distinguish the S-nitroso-form of a cysteine residue from the sulfhydryl-form or from a methionine thioether. Comparison of the sulfur K-edge spectra of thiolate, thiol, thioether, and S-nitroso thiolate compounds indicates high sensitivity of energy positions and intensities of XAS pre-edge features as determined by the electronic environment of the sulfur absorber. A new experimental setup is being developed for reaching the in vivo concentration range of S-nitroso thiol levels in biological samples. 相似文献
6.
Julian A. Rees Aleksandra Wandzilak Dimitrios Maganas Nicole I. C. Wurster Stefan Hugenbruch Joanna K. Kowalska Christopher J. Pollock Frederico A. Lima Kenneth D. Finkelstein Serena DeBeer 《Journal of biological inorganic chemistry》2016,21(5-6):793-805
A series of vanadium compounds was studied by K-edge X-ray absorption (XAS) and K\(\beta \) X-ray emission spectroscopies (XES). Qualitative trends within the datasets, as well as comparisons between the XAS and XES data, illustrate the information content of both methods. The complementary nature of the chemical insight highlights the success of this dual-technique approach in characterizing both the structural and electronic properties of vanadium sites. In particular, and in contrast to XAS or extended X-ray absorption fine structure (EXAFS), we demonstrate that valence-to-core XES is capable of differentiating between ligating atoms with the same identity but different bonding character. Finally, density functional theory (DFT) and time-dependent DFT calculations enable a more detailed, quantitative interpretation of the data. We also establish correction factors for the computational protocols through calibration to experiment. These hard X-ray methods can probe vanadium ions in any oxidation or spin state, and can readily be applied to sample environments ranging from solid-phase catalysts to biological samples in frozen solution. Thus, the combined XAS and XES approach, coupled with DFT calculations, provides a robust tool for the study of vanadium atoms in bioinorganic chemistry. 相似文献
7.
Xiaohui Zhu Lucas Le Nagard Dennis A. Bazylinski Viviana Morillo Fernanda Abreu 《Geomicrobiology journal》2018,35(3):215-226
Scanning transmission X-ray microscopy at the Fe 2p (L2,3), O1s, C1s, and S2p edges was used to study greigite magnetosomes and other cellular content of a magnetotactic bacterium known as a multicellular magnetotactic prokaryote (MMP). X-ray absorption spectrum (XAS) and X-ray magnetic circular dichroism (XMCD) spectra of greigite (Fe3S4) nanoparticles, synthesized via a hydrothermal method, were measured. Although XAS of the synthetic greigite nanoparticles and biotic magnetosome crystals in MMPs are slightly different due to partial oxidation of the MMP greigite, the XMCD spectra of the two materials are in good agreement. The Fe 2p XAS and XMCD spectra of Fe3S4 are quite different from those of its oxygen analog, magnetite (Fe3O4), suggesting Fe3S4 has a different electronic and magnetic structure than Fe3O4 despite having the same crystal structure. Sulfate and sulfide species were also identified in MMPs, both of which are likely involved in sulfur metabolism. 相似文献
8.
Speciation of sulfur from filamentous microbial mats from sulfidic cave springs using X-ray absorption near-edge spectroscopy 总被引:1,自引:0,他引:1
Most transformations within the sulfur cycle are controlled by the biosphere, and deciphering the abiotic and biotic nature and turnover of sulfur is critical to understand the geochemical and ecological changes that have occurred throughout the Earth's history. Here, synchrotron radiation-based sulfur K-edge X-ray absorption near-edge structure (XANES) spectroscopy is used to examine sulfur speciation in natural microbial mats from two aphotic (cave) settings. Habitat geochemistry, microbial community compositions, and sulfur isotope systematics were also evaluated. Microorganisms associated with sulfur metabolism dominated the mats, including members of the Epsilonproteobacteria and Gammaproteobacteria. These groups have not been examined previously by sulfur K-edge XANES. All of the mats consisted of elemental sulfur, with greater contributions of cyclo-octasulfur (S8) compared with polymeric sulfur (Smicro). While this could be a biological fingerprint for some bacteria, the signature may also indicate preferential oxidation of Smicro and S8 accumulation. Higher sulfate content correlated to less S8 in the presence of Epsilonproteobacteria. Sulfur isotope compositions confirmed that sulfur content and sulfur speciation may not correlate to microbial metabolic processes in natural samples, thereby complicating the interpretation of modern and ancient sulfur records. 相似文献
9.
In situ analysis of sulfur species in sulfur globules produced from thiosulfate by Thermoanaerobacter sulfurigignens and Thermoanaerobacterium thermosulfurigenes
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Lee YJ Prange A Lichtenberg H Rohde M Dashti M Wiegel J 《Journal of bacteriology》2007,189(20):7525-7529
The Firmicutes Thermoanaerobacter sulfurigignens and Thermoanaerobacterium thermosulfurigenes convert thiosulfate, forming sulfur globules inside and outside cells. X-ray absorption near-edge structure analysis revealed that the sulfur consisted mainly of sulfur chains with organic end groups similar to sulfur formed in purple sulfur bacteria, suggesting the possibility that the process of sulfur globule formation by bacteria is an ancient feature. 相似文献
10.
Tenderholt AL Szilagyi RK Holm RH Hodgson KO Hedman B Solomon EI 《Journal of inorganic biochemistry》2007,101(11-12):1594-1600
Molybdenum- or tungsten-containing enzymes catalyze oxygen atom transfer reactions involved in carbon, sulfur, or nitrogen metabolism. It has been observed that reduction potentials and oxygen atom transfer rates are different for W relative to Mo enzymes and the isostructural Mo/W complexes. Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations on [Mo(V)O(bdt)(2)](-) and [W(V)O(bdt)(2)](-), where bdt=benzene-1,2-dithiolate(2-), have been used to determine that the energies of the half-filled redox-active orbital, and thus the reduction potentials and MO bond strengths, are different for these complexes due to relativistic effects in the W sites. 相似文献
11.
Dahl C Schulte A Stockdreher Y Hong C Grimm F Sander J Kim R Kim SH Shin DH 《Journal of molecular biology》2008,384(5):1287-1300
Many environmentally important photo- and chemolithoautotrophic bacteria accumulate globules of polymeric, water-insoluble sulfur as a transient product during oxidation of reduced sulfur compounds. Oxidation of this sulfur requires the concerted action of Dsr proteins. However, individual functions and interplay of these proteins are largely unclear. We proved with a ΔdsrE mutant experiment that the cytoplasmic α2β2γ2-structured protein DsrEFH is absolutely essential for the oxidation of sulfur stored in the intracellular sulfur globules of the purple sulfur bacterial model organism Allochromatium vinosum. The ability to degrade stored sulfur was fully regained upon complementation with dsrEFH in trans. The crystal structure of DsrEFH was determined at 2.5 Å resolution to assist functional assignment in detail. In conjunction with phylogenetic analyses, two different types of putative active sites were identified in DsrE and DsrH and shown to be characteristic for sulfur-oxidizing bacteria. Conserved Cys78 of A. vinosum DsrE corresponds to the active cysteines of Escherichia coli YchN and TusD. TusBCD and the protein TusE are parts of sulfur relay system involved in thiouridine biosynthesis. DsrEFH interacts with DsrC, a TusE homologue encoded in the same operon. The conserved penultimate cysteine residue in the carboxy-terminus of DsrC is essential for the interaction. Here, we show that Cys78 of DsrE is strictly required for interaction with DsrC while Cys20 in the putative active site of DsrH is dispensable for that reaction. In summary, our findings point at the occurrence of sulfur transfer reactions during sulfur oxidation via the Dsr proteins. 相似文献
12.
M. Giorgetti I. Ascone M. Berrettoni P. Conti S. Zamponi R. Marassi 《Journal of biological inorganic chemistry》2000,5(2):156-166
An in situ X-ray absorption spectroscopy (XAS) spectroelectrochemical study of aquocobalamin (system B12a-B12r-B12s) has been carried out in aqueous solutions buffered at different pH values. To the best of our knowledge, this is the first
structural study of aquocobalamin at room temperature under controlled oxidation conditions. Most of the previous work was
in fact performed using frozen samples chemically treated to produce the species. The spectroelectrochemical approach offers
several advantages: (1) the reduction products may be studied without poisoning the system with chemical reductive reagents
and (2) any possible variation of the oxidation state owing to the electrons produced by the incident beam is avoided as the
electrode, under potentiostatic control, acts as a scavenger. The spectroelectrochemical approach, together with more careful
data analysis, has led to an improved interpretation of the XAS data. These conditions were not met in previous works where
the oxidation state was not controlled and multiple scattering contributions were not taken into account. The general shape
of the XAS spectra of the different species is not greatly affected by pH. A signature for the base-off square-planar coordination
has been evidenced for the Co(II) compound at basic pH. A new signature for Co(I), indicating square-planar coordination,
has been identified on the experimental spectra and simulated in theoretical X-ray absorption near-edge structure (XANES)
studies. The flexibility of the electrochemical approach, that permits to unambiguously establish the formal oxidation state,
has led to very reliable values for energy shift and peak intensity variations. The experimental XANES and extended X-ray
absorption fine structure (EXAFS) spectra with a very good signal-to-noise ratio have been processed using the GNXAS package
that takes into account multiple scattering contributions. EXAFS and XANES independent analysis result in the same structural
model. The reduction from Co(III) to Co(II) produces the most significant structural changes: the cobalt coordination number
decreases from six to five, and the edge position shifts by 2.4±0.3 eV. In addition, the XANES spectra are strongly modified.
The reduction from Co(II) to Co(I) produces mainly electronic effects with no apparent change of the coordination number.
A discussion of the limits and potentialities of EXAFS in this type of study has also been included.
Received: 26 July 1999 / Accepted: 22 October 1999 相似文献
13.
He Huan Xia Jin-lan Huang Guan-hua Jiang Hong-Chen Tao Xiu-Xiang Zhao Yi-Dong He Wei 《World journal of microbiology & biotechnology》2011,27(8):1927-1931
Elemental sulfur bio-oxidation by the typical acidophilic sulfur-oxidizing microbe Acidithiobacillus ferrooxidans was investigated by using the technique of sulfur K-edge XANES spectroscopy. Our results showed that the majority of elemental
sulfur altered by A. ferrooxidans was dissolved into the organic phase containing carbon disulfide, while a part of it floated. The fitted results of sulfur
K-edge XANES spectrum of the floated sulfur showed that the floating part of the elemental sulfur powder was converted to
polymeric sulfur and the relative concentration of sulfur in cyclo-octasulfur S8 and polymeric sulfur was 37.2 and 62.8%, respectively. It seems that the cyclo-octasulfur is converted to the polymeric sulfur
and this appears to be necessary for oxidation of elemental sulfur by A. ferrooxidans. The results have important implications for our understanding of the mechanisms for bio-oxidation of elemental sulfur. 相似文献
14.
P. Anil Kumar T. N. R. Srinivas Ch. Sasikala Ch. V. Ramana J. Süling J. F. Imhoff 《World journal of microbiology & biotechnology》2007,23(3):393-399
A novel selective enrichment method is described for phototrophic green sulfur bacteria even in the presence of purple sulfur
and purple nonsulfur bacteria using sulfanilate, which was discovered during efforts to selectively isolate sulfanilate-metabolizing
anoxygenic phototrophic bacteria from marine habitats. Samples for these experiments were obtained from beaches, saltpans,
subsurface mangrove soils, fish and prawn aquaculture ponds and backwaters of the East and West coasts of India. Photoorganoheterotrophic
and photolithoautotrophic enrichments in the absence of sulfanilate predominantly yielded purple bacterial enrichments. In
contrast, photolithoautotrophic enrichments in the presence of sulfanilate yielded green-colored enrichments from the same
samples. Whole cell absorption spectra of the enrichment cultures revealed the presence of bacteriochlorophyll c and thus green phototrophic bacteria. Microscopic observation demonstrated the presence of sulfur globules outside the bacterial
cells and the presence of non-motile cells, some of which had prosthecae. 16S rDNA sequences obtained from green sulfur bacterial
strains isolated from enrichment cultures confirmed the presence of representatives of the green sulfur bacterial genera Prosthecochloris and Chlorobaculum. The selective pressure of sulfanilate exerted through inhibition of phototrophic purple sulfur bacteria was demonstrated
by inhibition studies using the purple sulfur bacteria Marichromatium indicum JA100 and Marichromatium sp. JA120 (JCM 13533) and the green sulfur bacterium Prosthecochloris sp. JAGS6 (JCM 13299). 相似文献
15.
Investigation of Elemental Sulfur Speciation Transformation Mediated by Acidithiobacillus ferrooxidans 总被引:1,自引:0,他引:1
Huan He Cheng-Gui Zhang Jin-Lan Xia An-An Peng Yi Yang Hong-Chen Jiang Lei Zheng Chen-Yan Ma Yi-Dong Zhao Zhen-Yuan Nie Guan-Zhou Qiu 《Current microbiology》2009,58(4):300-307
The speciation transformation of elemental sulfur mediated by the leaching bacterium Acidithiobacillus ferrooxidans was investigated using an integrated approach including scanning electron microscopy, transmission electron microscopy, Fourier
transform infrared spectroscopy, energy dispersive X-ray spectroscopy, and X-ray absorption near edge spectroscopy (XANES).
Our results showed that when grown on elemental sulfur powder, At. ferrooxidans ATCC23270 cells were first attached to sulfur particles and modified the surface sulfur with some amphiphilic compounds.
In addition, part of the elemental sulfur powder might be converted to polysulfides. Furthermore, sulfur globules were accumulated
inside the cells. XANES spectra of these cells suggested that these globules consisted of elemental sulfur bound to thiol
groups of protein.
Huan He and Cheng-Gui Zhang made equal contributions to this paper. 相似文献
16.
Microbial Desulfurization of a Crude Oil Middle-Distillate Fraction: Analysis of the Extent of Sulfur Removal and the Effect of Removal on Remaining Sulfur 总被引:4,自引:2,他引:4
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M. J. Grossman M. K. Lee R. C. Prince K. K. Garrett G. N. George I. J. Pickering 《Applied microbiology》1999,65(1):181-188
Rhodococcus sp. strain ECRD-1 was evaluated for its ability to desulfurize a 232 to 343°C middle-distillate (diesel range) fraction of Oregon basin (OB) crude oil. OB oil was provided as the sole source of sulfur in batch cultures, and the extent of desulfurization and the chemical fate of the residual sulfur in the oil after treatment were determined. Gas chromatography (GC), flame ionization detection, and GC sulfur chemiluminesce detection analysis were used to qualitatively evaluate the effect of Rhodococcus sp. strain ECRD-1 treatment on the hydrocarbon and sulfur content of the oil, respectively. Total sulfur was determined by combustion of samples and measurement of released sulfur dioxide by infrared absorption. Up to 30% of the total sulfur in the middle distillate cut was removed, and compounds across the entire boiling range of the oil were affected. Sulfur K-edge X-ray absorption-edge spectroscopy was used to examine the chemical state of the sulfur remaining in the treated OB oil. Approximately equal amounts of thiophenic and sulfidic sulfur compounds were removed by ECRD-1 treatment, and over 50% of the sulfur remaining after treatment was in an oxidized form. The presence of partially oxidized sulfur compounds indicates that these compounds were en route to desulfurization. Overall, more than two-thirds of the sulfur had been removed or oxidized by the microbial treatment. 相似文献
17.
Ryan B. Boysen 《Inorganica chimica acta》2008,361(4):1047-1058
X-ray absorption spectroscopy (XAS) is a synchrotron-based experimental technique that provides information about geometric and electronic structures of transition metal complexes. Combination of metal L-edge and ligand K-edge XAS has the potential to define the complete experimental ground state electronic structures for metal complexes with unoccupied d manifolds. We developed a quantitative treatment for Pd L-edge spectroscopy on the basis of the well-established chlorine K-edge XAS for a series of chloropalladium complexes that are pre-catalysts in various organic transformations. We found that Pd-Cl bonds are highly covalent, such as 24 ± 2%, 34 ± 3%, and 48 ± 4% chloride 3p character for each Pd-Cl bond in [PdCl4]2−, [PdCl6]2−, and PdCl2, respectively. Pd(2p → 4d) transition dipole integrals of 20.8 (SSRL)/16.9 (ALS) eV and 14.1 (SSRL)/11.9 (ALS) eV were determined using various combinations of L-edges for Pd(II) and Pd(IV), respectively. Application of metal-ligand covalency and transition dipole integrals were demonstrated for the example of bridging chloride ligands in PdCl2. Our work lays the foundation for extending the quantitative treatment to other catalytically important ligands, such as phosphine, phosphite, olefin, amine, and alkyl in order to correlate the electronic structures of palladium complexes with their catalytic activity. 相似文献
18.
K-edge X-ray absorption and EPR spectroscopies were used to test the variation in blood cell vanadium between and within specimens of the tunicate Ascidia ceratodes from Bodega Bay, California. Intracellular vanadium was speciated by fitting the XAS spectra of whole blood cells with linear combinations of the XAS spectra of models. Blood cell samples representing one specimen each, respectively, revealed 92.5 and 38.7% of endogenous vanadium as [V(H(2)O)(6)](3+), indicating dissimilar distributions. Conversely, vanadium distributions within blood cell samples respectively representing one and six specimens proved very similar. The derived array of V(III) complexes was consistent with multiple intracellular regions that differ both in pH and c(sulfate), both within and between specimens. No systematic effect on vanadium distribution was apparent on mixing blood cells. EPR and XAS results indicated at least three forms of endogenous vanadyl ion, two of which may be dimeric. An inverse linear correlation was found between soluble and complexed forms of vanadyl ion, implying co-regulation. The EPR A value of endogenous vanadyl ion [A(0)=(1.062+/-0.008)x10(-2) cm(-1)] was marginally different from that representing Monterey Bay A. ceratodes [A(0)=(1.092+/-0.006) x10(-2) cm(-1)]. Comparisons indicate that Bodega Bay A. ceratodes maintain V(III) in a more acidic intracellular environment on average than do those from Monterey Bay, showing variation across populations. Blood cell vanadium thus noticeably diverges at all organismal levels among A. ceratodes. 相似文献
19.
Simon J. George Yisong Guo Stephan Friedrich Thomas Rauchfuss Jonas C. Peters Valerie Scott Christine M. Thomas 《Inorganica chimica acta》2008,361(4):1157-1165
Under intense soft X-ray irradiation, we have observed time-dependent changes in the soft X-ray spectra of virtually all the Fe coordination complexes that we have examined, indicating chemical transformation of the compound under study. Each compound, with oxidation states ranging from Fe(IV) to Fe(0), has been studied with either Fe L-edge spectroscopy or N K-edge spectroscopy. We find that very often a well-defined spectroscopic change occurs, at least initially, which is apparently capable of straightforward interpretation in terms of X-ray induced photoreduction, photooxidation or ligand photolysis. We briefly discuss the probable chemical nature of the changes and then estimate the rate of chemical change, thereby establishing the necessary radiation dose. We also demonstrate that the photochemistry not only depends on the Fe oxidation state but also the coordination chemistry of the complex. It seems that a proper understanding of such X-ray photochemical effects could well greatly assist the assignment of soft X-ray spectra of uncharacterized metal sites. 相似文献
20.
The quantum efficiency of photosynthesis by the green sulfur bacterium, Chlorobium thiosulfatophilum, has been determined in systems in which thiosulfate, tetrathionate, and molecular hydrogen served as electron donors. It was found that about 10 ± 1 quanta are used for the assimilation of 1 molecule of CO2, and that the quantum number is independent of the nature of the electron donor. These results are considered as support for the view that also in the bacterial photosyntheses the primary photochemical reaction consists in the photolysis of H2O, and that the chemical energy released during the oxidation of the electron donor is not utilized for CO2 assimilation. Hence the photosynthetic processes of the green sulfur bacteria are thermodynamically less efficient than is green plant photosynthesis. 相似文献