Novel genes of the dsr gene cluster and evidence for close interaction of Dsr proteins during sulfur oxidation in the phototrophic sulfur bacterium Allochromatium vinosum

Seven new genes designated dsrLJOPNSR were identified immediately downstream of dsrABEFHCMK, completing the dsr gene cluster of the phototrophic sulfur bacterium Allochromatium vinosum D (DSM 180(T)). Interposon mutagenesis proved an essential role of the encoded proteins for the oxidation of intracellular sulfur, an obligate intermediate during the oxidation of sulfide and thiosulfate. While dsrR and dsrS encode cytoplasmic proteins of unknown function, the other genes encode a predicted NADPH:acceptor oxidoreductase (DsrL), a triheme c-type cytochrome (DsrJ), a periplasmic iron-sulfur protein (DsrO), and an integral membrane protein (DsrP). DsrN resembles cobyrinic acid a,c-diamide synthases and is probably involved in the biosynthesis of siro(heme)amide, the prosthetic group of the dsrAB-encoded sulfite reductase. The presence of most predicted Dsr proteins in A. vinosum was verified by Western blot analysis. With the exception of the constitutively present DsrC, the formation of Dsr gene products was greatly enhanced by sulfide. DsrEFH were purified from the soluble fraction and constitute a soluble alpha(2)beta(2)gamma(2)-structured 75-kDa holoprotein. DsrKJO were purified from membranes pointing at the presence of a transmembrane electron-transporting complex consisting of DsrKMJOP. In accordance with the suggestion that related complexes from dissimilatory sulfate reducers transfer electrons to sulfite reductase, the A. vinosum Dsr complex is copurified with sulfite reductase, DsrEFH, and DsrC. We therefore now have an ideal and unique possibility to study the interaction of sulfite reductase with other proteins and to clarify the long-standing problem of electron transport from and to sulfite reductase, not only in phototrophic bacteria but also in sulfate-reducing prokaryotes.     

Importance of the DsrMKJOP complex for sulfur oxidation in Allochromatium vinosum and phylogenetic analysis of related complexes in other prokaryotes

In the phototrophic sulfur bacterium Allochromatium vinosum, sulfur of oxidation state zero stored in intracellular sulfur globules is an obligate intermediate during the oxidation of sulfide and thiosulfate. The proteins encoded in the dissimilatory sulfite reductase (dsr) locus are essential for the oxidation of the stored sulfur. DsrMKJOP form a membrane-spanning complex proposed to accept electrons from or to deliver electrons to cytoplasmic sulfur-oxidizing proteins. In frame deletion mutagenesis showed that each individual of the complex-encoding genes is an absolute requirement for the oxidation of the stored sulfur in Alc. vinosum. Complementation of the ΔdsrJ mutant using the conjugative broad host range plasmid pBBR1-MCS2 and the dsr promoter was successful. The importance of the DsrMKJOP complex is underlined by the fact that the respective genes occur in all currently sequenced genomes of sulfur-forming bacteria such as Thiobacillus denitrificans and Chlorobaculum tepidum. Furthermore, closely related genes are present in the genomes of sulfate- and sulfite-reducing prokaryotes. A phylogenetic analysis showed that most dsr genes from sulfide oxidizers are clearly separated of those from sulfate reducers. Surprisingly, the dsrMKJOP genes of the Chlorobiaceae all cluster together with those of the sulfate/sulfite-reducing prokaryotes, indicating a lateral gene transfer at the base of the Chlorobiaceae.Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

In situ analysis of sulfur in the sulfur globules of phototrophic sulfur bacteria by X-ray absorption near edge spectroscopy.

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.     

Coexistence of aerobic chemotrophic and anaerobic phototrophic sulfur bacteria under oxygen limitation

Abstract: The aerobic chemotrophic sulfur bacterium Thiobacillus thioparus T5 and the anaerobic phototrophic sulfur bacterium Thiocapsa roseopersicina M1 were co-cultured in continuously illuminated chemostats at a dilution rate of 0.05 h⁻¹. Sulfide was the only externally supplied electron donor, and oxygen and carbon dioxide served as electron acceptor and carbon source, respectively. Steady states were obtained with oxygen supplies ranging from non-limiting amounts (1.6 mol O₂ per mol sulfide, resulting in sulfide limitation) to severe limitation (0.65 mol O₂ per mol sulfide). Under sulfide limitation Thiocapsa was competitively excluded by Thiobacillus and washed out. Oxygen/sulfide ratios between 0.65 and 1.6 resulted in stable coexistence. It could be deduced that virtually all sulfide was oxidized by Thiobacillus . The present experiments showed that Thiocapsa is able to grow phototrophically on the partially oxidized products of Thiobacillus . In pure Thiobacillus cultures in steady state extracellular zerovalent sulfur accumulated, in contrast to mixed cultures. This suggests that a soluble form of sulfur at the oxidation state of elemental sulfur is formed by Thiobacillus as intermediate. As a result, under oxygen limitation colorless sulfur bacteria and purple sulfur bacteria do not competitively exclude each other but can coexist. It was shown that its ability to use partially oxidized sulfur compounds, formed under oxygen limiting conditions by Thiobacillus , helps explain the bloom formation of Thiocapsa in marine microbial mats.     

Characterization of purple sulfur bacteria from the South Andros Black Hole cave system: highlights taxonomic problems for ecological studies among the genera Allochromatium and Thiocapsa

A dense 1 m thick layer of phototrophic purple sulfur bacteria is present at the pycnocline (17.8 m depth) in the meromictic South Andros Black Hole cave system (Bahamas). Two purple sulfur bacteria present in samples collected from this layer have been identified as belonging to the family Chromatiaceae. One isolate (BH-1), pink coloured, is non-motile, non-gas vacuolated, 2-3 microm in diameter and surrounded by a capsule. The other isolates (BH-2 and BH-2.4), reddish-brown coloured, are small celled (4 microm x 2 microm), motile by means of a single polar flagellum. In both isolates (BH-1 and BH-2), the intracellular photosynthetic membranes are of the vesicular type and bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series are present. Both isolates grow well in the presence of sulfide and carbon dioxide in the light. During photoautotrophic growth sulfur globules are stored intracellularly as intermediate oxidation products. According to the 16S rRNA gene sequence data the isolates belong to the genera Thiocapsa and Allochromatium. However, at the species level a number of inconsistencies exist between the phenotypic and phylogenetic data, highlighting taxonomic problems within these genera. These inconsistencies may have implications for microbiologists studying the ecology of anoxygenic phototrophs. For ecologists studying the functioning of an ecosystem it may not be particularly important to know whether a specific isolate belongs to one species or another. However, if one wants to study the role of different populations within a particular functional group then the species concept is important. This study demonstrates that further work is still required on the taxonomy of purple sulfur bacteria in order that microbial ecologists are able to accurately identify a population/species isolated from hitherto undescribed aquatic ecosystems.     

Insight into the molecular mechanism of the sulfur oxidation process by reverse sulfite reductase (rSiR) from sulfur oxidizer <Emphasis Type="Italic">Allochromatium vinosum</Emphasis>

Sulfur metabolism is one of the oldest known biochemical processes. Chemotrophic or phototrophic proteobacteria, through the dissimilatory pathway, use sulfate, sulfide, sulfite, thiosulfate or elementary sulfur by either reductive or oxidative mechanisms. During anoxygenic photosynthesis, anaerobic sulfur oxidizer Allochromatium vinosum forms sulfur globules that are further oxidized by dsr operon. One of the key redox enzymes in reductive or oxidative sulfur metabolic pathways is the DsrAB protein complex. However, there are practically no reports to elucidate the molecular mechanism of the sulfur oxidation process by the DsrAB protein complex from sulfur oxidizer Allochromatium vinosum. In the present context, we tried to analyze the structural details of the DsrAB protein complex from sulfur oxidizer Allochromatium vinosum by molecular dynamics simulations. The molecular dynamics simulation results revealed the various types of molecular interactions between DsrA and DsrB proteins during the formation of DsrAB protein complex. We, for the first time, predicted the mode of binding interactions between the co-factor and DsrAB protein complex from Allochromatium vinosum. We also compared the binding interfaces of DsrAB from sulfur oxidizer Allochromatium vinosum and sulfate reducer Desulfovibrio vulgaris. This study is the first to provide a comparative aspect of binding modes of sulfur oxidizer Allochromatium vinosum and sulfate reducer Desulfovibrio vulgaris.     

Cytoplasmic sulfurtransferases in the purple sulfur bacterium Allochromatium vinosum: evidence for sulfur transfer from DsrEFH to DsrC

While the importance of sulfur transfer reactions is well established for a number of biosynthetic pathways, evidence has only started to emerge that sulfurtransferases may also be major players in sulfur-based microbial energy metabolism. Among the first organisms studied in this regard is the phototrophic purple sulfur bacterium Allochromatium vinosum. During the oxidation of reduced sulfur species to sulfate this Gammaproteobacterium accumulates sulfur globules. Low molecular weight organic persulfides have been proposed as carrier molecules transferring sulfur from the periplasmic sulfur globules into the cytoplasm where it is further oxidized via the "Dsr" (dissimilatory sulfite reductase) proteins. We have suggested earlier that the heterohexameric protein DsrEFH is the direct or indirect acceptor for persulfidic sulfur imported into the cytoplasm. This proposal originated from the structural similarity of DsrEFH with the established sulfurtransferase TusBCD from E. coli. As part of a system for tRNA modification TusBCD transfers sulfur to TusE, a homolog of another crucial component of the A. vinosum Dsr system, namely DsrC. Here we show that neither DsrEFH nor DsrC have the ability to mobilize sulfane sulfur directly from low molecular weight thiols like thiosulfate or glutathione persulfide. However, we demonstrate that DsrEFH binds sulfur specifically to the conserved cysteine residue DsrE-Cys78 in vitro. Sulfur atoms bound to cysteines in DsrH and DsrF were not detected. DsrC was exclusively persulfurated at DsrC-Cys111 in the penultimate position of the protein. Most importantly, we show that persulfurated DsrEFH indeed serves as an effective sulfur donor for DsrC in vitro. The active site cysteines Cys78 of DsrE and Cys20 of DsrH furthermore proved to be essential for sulfur oxidation in vivo supporting the notion that DsrEFH and DsrC are part of a sulfur relay system that transfers sulfur from a persulfurated carrier molecule to the dissimilatory sulfite reductase DsrAB.     

Competition between anoxygenic phototrophic bacteria and colorless sulfur bacteria in a microbial mat

Abstract The populations of chemolithoautotrophic (colorless) sulfur bacteria and anoxygenic phototrophic bacteria were enumerated in a marine microbial mat. The highest population densities were found in the 0–5 mm layer of the mat: 2.0 × 10⁹ cells cm⁻³ sediment, and 4.0 × 10⁷ cells cm⁻³ sediment for the colorless sulfur bacteria and phototrophs, respectively. Kinetic parameters for thiosulfate-limited growth were assessed for Thiobacillus thioparus T5 and Thiocapsa roseopersicina M1, both isolated from microbial mats. For Thiobacillus T5, growing at a constant oxygen concentration of 43 μmol l⁻¹, μ_max was 0.336 h⁻¹ and K _s 0.8 μmol l⁻¹. Phototrophically grown Thiocapsa strain M1 displayed a μ_max of 0.080 h⁻¹ and a K _s of 8 μmol l⁻¹ when anoxically grown under thiosulfate limitation. In a competition experiment with thiosulfate as electron donor, Thiocapsa became dominant during a 10-h oxic/14-h anoxic regimen at continuous illumination, despite the higher affinity for thiosulfate of Thiobacillus .     

A Benthic Gradient Chamber for culturing phototrophic sulfur bacteria on reconstituted sediments

Abstract: The growth of phototrophic sulfur bacteria in benthic systems is restricted to well-defined layers within the sedimentary oxygen, sulfide, pH and light gradients. In order to culture these microorganisms under more ecologically relevant conditions, we have developed a Benthic Gradient Chamber (BGC) in which phototrophic sulfur bacteria can be grown within experimentally imposed solute and light gradients. The new autoclavable device is composed of a reconstituted sand core sandwiched in between a lower anoxic sulfide-containing compartment and an upper oxic compartment. The core can be illuminated from above by a collimated light beam. An axenic biofilm of Thiocapsa roseopersicina strain EP 2204 developed from a tiny inoculum within the sand core, using a 5-week incubation period and a 16:8 h light/dark illumination regime. The metabolic activities in this biofilm were inferred from the analyses of oxygen, sulfide and pH profiles, and their shifts during light-dark cycles.     

The phototrophic community found in Lake Khilganta (an alkaline saline lake located in the southeastern Transbaikal region)

The structure of the phototrophic community found in Lake Khilganta (the Agin-Buryat Autonomous Area), a shallow saline soda lake (depth, 35-45 cm; water mineralization, 45 g/l; alkalinity, 30 mg-equiv/l; pH 9.5) has been studied. The bottom of the lake is covered with a 10- to 15-mm microbial mat, whose basis is formed by the filamentous cyanobacterium Microcoleus chthonoplastes. The mat exhibits pronounced layering and contains a significant amount of minerals. Six zones, which have characteristic colors and consistencies and are composed of intermittent layers, have been identified along the vertical profile. Live phototrophic bacteria have been found in the three upper zones. The bulk of the cyanobacteria is concentrated in the upper zone. In the lower zones, the development of purple bacteria has been observed. The diurnal dynamics of the vertical distribution of phototrophic microorganisms, which results from variations in the physicochemical environmental parameters, is described. Ectothiorhodospira sp. are dominant among the anoxyphotobacteria present. Their number, determined according to the inoculation method, is 10(6)-10(7) cells/ml. The purple bacteria of the genera Allochromatium, Thiocapsa, and Rhodovulum are also present. Experiments with isolated pure cultures have shown that the anoxygenic photosynthetic bacteria of Lake Khilganta are halotolerant and alkalitolerant or alkaliphilic. In liquid enrichment cultures, at pH 9.5, the ratio of anoxyphotobacteria species is close to that observed in the lake. When the pH is increased to 10.4, it is Ectothiorhodospira, which is the most adapted to life under increased mineralization and alkalinity, that predominantly develops. Photosynthetic activity has been observed in the three upper mat zones and constitutes, on average, 1.5 g C/(m2 h); the share of anoxygenic photosynthesis accounts for 75-95% of the total productivity. The main role in sulfide oxidation belongs to the phototrophic anoxyphotobacteria and cyanobacteria. In terms of the physicochemical conditions and structure of the phototrophic community, Lake Khilganta is similar to shallow saline water bodies of marine origin. The main differences consist in the increased alkalinity and in the consequent prevalence of alkaliphilic and alkalitolerant microorganisms and in the absence of representatives of the neutrophilic group of green sulfur bacteria.     

Sulfide removal and elemental sulfur recycling from a sulfide-polluted medium by Allochromatium vinosum strain 21D.

Phototrophic purple sulfur bacteria oxidize sulfide to elemental sulfur, which is stored as intracellular sulfur globules. The mutant Allochromatium vinosum strain 21D, containing an inactivated dsrB gene, is unable to further oxidize intracellularly stored sulfur to sulfate. This mutant was used as a biocatalyst in a biotechnological process to eliminate sulfide from synthetic wastewater and to recycle elemental sulfur as a raw material. For this purpose, the mutant was grown in an illuminated 5-liter bioreactor (30 microE/m2/s PAR) at 30 degrees C for 61 days in anoxic phototrophic medium. The process of sulfide removal was semi-continuous and consisted of three consecutive fed-batch sections. Sulfide was repeatedly added into the bioreactor and oxidized by the cells to sulfur. In the presence of the mutant, no unwanted sulfate was produced during sulfide removal. A maximum sulfide removal rate of 49.3 microM/h, a maximum sulfide removal efficiency of 98.7%, and 60.4% sulfur recycling were achieved.     

Inorganic sulfur oxidizing system in green sulfur bacteria

Green sulfur bacteria use various reduced sulfur compounds such as sulfide, elemental sulfur, and thiosulfate as electron donors for photoautotrophic growth. This article briefly summarizes what is known about the inorganic sulfur oxidizing systems of these bacteria with emphasis on the biochemical aspects. Enzymes that oxidize sulfide in green sulfur bacteria are membrane-bound sulfide-quinone oxidoreductase, periplasmic (sometimes membrane-bound) flavocytochrome c sulfide dehydrogenase, and monomeric flavocytochrome c (SoxF). Some green sulfur bacteria oxidize thiosulfate by the multienzyme system called either the TOMES (thiosulfate oxidizing multi-enzyme system) or Sox (sulfur oxidizing system) composed of the three periplasmic proteins: SoxB, SoxYZ, and SoxAXK with a soluble small molecule cytochrome c as the electron acceptor. The oxidation of sulfide and thiosulfate by these enzymes in vitro is assumed to yield two electrons and result in the transfer of a sulfur atom to persulfides, which are subsequently transformed to elemental sulfur. The elemental sulfur is temporarily stored in the form of globules attached to the extracellular surface of the outer membranes. The oxidation pathway of elemental sulfur to sulfate is currently unclear, although the participation of several proteins including those of the dissimilatory sulfite reductase system etc. is suggested from comparative genomic analyses.     

Thiosulfate, polythionates and elemental sulfur assimilation and reduction in the bacterial world

Abstract Among sulfur compounds, thiosulfate and polythionates are present at least transiently in many environments. These compounds have a similar chemical structure and their metabolism appears closely related. They are commonly used as energy sources for photoautotrophic or chemolithotrophic microorganisms, but their assimilation has been seldom studied and their importance in bacterial physiology is not well understood. Almost all bacterial strains are able to cleave these compounds since they possess thiosulfate sulfur transferase, thiosulfate reductace or S -sulfocysteine synthase activities. However, the role of these enzymes in the assimilation of thiosulfate or polythionates has not always been clearly established.
Elemental sulfur is, on the contrary, very common in the environmental. It is an energy source for sulfur-reducing eubacteria and archaebacteria and many sulfur-oxidizing archaebacteria. A phenomenon still not well understood is the 'excessive assimilatory sulfur metabolism' as observed in methanogens which perform a sulfur reduction which exceeds their anabolic needs without any apparent benefit. In heterotrophs, assimilation of elemental sulfur is seldom described and it is uncertain whether this process actually has a physiological significance.
Thus, reduction of thiosulfate and elemental sulfur is a common by incompletely understood feature among bacteria. These activities could give bacteria a selective advantage, but futher investigations are needed to clarify this possibility. Presence of thiosulfate, polythionates and sulfur reductase activities does not imply obligatorily that these activities play a role in thiosulfate, polythionates or sulfur assimilation as these compounds could be merely intermediates in bacterial metabolism. The possibility also exists that the assimilation of these sulfur compounds is just a side effect of an enzymatic activity with a completely different function.     

Genes involved in the biosynthesis of photosynthetic pigments in the purple sulfur photosynthetic bacterium Thiocapsa roseopersicina

A pigment mutant strain of the purple sulfur photosynthetic bacterium Thiocapsa roseopersicina BBS was isolated by plasposon mutagenesis. Nineteen open reading frame, most of which are thought to be genes involved in the biosynthesis of carotenoids, bacteriochlorophyll, and the photosynthetic reaction center, were identified surrounding the plasposon in a 22-kb-long chromosomal locus. The general arrangement of the photosynthetic genes was similar to that in other purple photosynthetic bacteria; however, the locations of a few genes occurring in this region were unusual. Most of the gene products showed the highest similarity to the corresponding proteins in Rubrivivax gelatinosus. The plasposon was inserted into the crtD gene, likely inactivating crtC as well, and the carotenoid composition of the mutant strain corresponded to the aborted spirilloxanthin pathway. Homologous and heterologous complementation experiments indicated a conserved function of CrtC and CrtD in the purple photosynthetic bacteria. The crtDC and crtE genes were shown to be regulated by oxygen, and a role of CrtJ in aerobic repression was suggested.