Prokaryotic sulfur oxidation

The behavior of nitrifying sludge in presence of sulfur compounds using a floating biofilm reactor

The tolerance, kinetic and oxidizing capability of a nitrifying sludge exposed to different initial concentrations of sulfide (1.7 to 18mg/L) was evaluated in batch experiments. A nitrifying sludge fed with ammonium and thiosulfate and produced in steady state conditions was used as inoculum. Sulfide induced a significant effect either on ammonium consumption rates or nitrite accumulation. In spite of the nitrifying kinetic was affected, the ammonium consumption efficiencies were close to 100%, with nitrate production yields around 1.0. The IC(50) value for ammonium oxidizing-process was 13mg/L of sulfide. Sulfide was oxidized in two steps: first sulfide was oxidized to elemental sulfur and afterward into sulfate. FISH oligonucleotide probes for Thiobacillusdenitrificans, Nitrosomonas spp., and Nitrobacter spp. were used in order to know if these bacteria were part of the microbial ecology. The obtained results showed that under nitrifying conditions are possible to carry out simultaneously two biological processes, nitrification and sulfur oxidation.

Production of hydrogen gas from light and the inorganic electron donor thiosulfate by Rhodopseudomonas palustris

A challenge for photobiological production of hydrogen gas (H(2)) as a potential biofuel is to find suitable electron-donating feedstocks. Here, we examined the inorganic compound thiosulfate as a possible electron donor for nitrogenase-catalyzed H(2) production by the purple nonsulfur phototrophic bacterium (PNSB) Rhodopseudomonas palustris. Thiosulfate is an intermediate of microbial sulfur metabolism in nature and is also generated in industrial processes. We found that R. palustris grew photoautotrophically with thiosulfate and bicarbonate and produced H(2) when nitrogen gas was the sole nitrogen source (nitrogen-fixing conditions). In addition, illuminated nongrowing R. palustris cells converted about 80% of available electrons from thiosulfate to H(2). H(2) production with acetate and succinate as electron donors was less efficient (40 to 60%), partly because nongrowing cells excreted the intermediary metabolite α-ketoglutarate into the culture medium. The fixABCX operon (RPA4602 to RPA4605) encoding a predicted electron-transfer complex is necessary for growth using thiosulfate under nitrogen-fixing conditions and may serve as a point of engineering to control rates of H(2) production. The possibility to use thiosulfate expands the range of electron-donating compounds for H(2) production by PNSBs beyond biomass-based electron donors.

Genome sequence of the marine alphaproteobacterium HTCC2150, assigned to the Roseobacter clade

Here we announce the genome sequence of a marine bacterium, HTCC2150, that was isolated off the Oregon coast using dilution-to-extinction culturing and that is affiliated with the Roseobacter clade. The 16S rRNA phylogeny showed that the strain was closely related to members of the RCA clade. The genome sequence suggests that strain HTCC2150 is an organoheterotroph carrying diverse metabolic potential, including a close relationship with phytoplankton.

Beyond the genome: functional studies of phototrophic sulfur oxidation

The increasing availability of complete genomic sequences for cultured phototrophic bacteria and assembled metagenomes from environments dominated by phototrophs has reinforced the need for a "post-genomic" analytical effort to test models of cellular structure and function proposed from genomic data. Comparative genomics has produced a testable model for pathways of sulfur compound oxidation in the phototrophic bacteria. In the case of sulfide, two enzymes are predicted to oxidize sulfide: sulfide:quinone oxidoreductase and flavocytochrome c sulfide dehydrogenase. However, these models do not predict which enzyme is important under what conditions. In Chlorobaculum tepidum, a model green sulfur bacterium, a combination of genetics and physiological analysis of mutant strains has led to the realization that this organism contains at least two active sulfide:quinone oxidoreductases and that there is significant interaction between sulfide oxidation and light harvesting. In the case of elemental sulfur, an organothiol intermediate of unknown structure has been proposed to activate elemental sulfur for transport into the cytoplasm where it can be oxidized or assimilated, and recent approaches using classical metabolite analysis have begun to shed light on this issue both in C. tepidum and the purple sulfur bacterium Allochromatium vinosum.

Ribulose-1,5-bisphosphate carboxylase/oxygenase genes as a functional marker for chemolithoautotrophic halophilic sulfur-oxidizing bacteria in hypersaline habitats

The presence and diversity of the cbb genes encoding the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) (a key enzyme of the Calvin–Benson cycle of autotrophic CO2 assimilation) were investigated in pure cultures of seven genera of halophilic chemolithoautotrophic sulfur-oxidizing bacteria (SOB) and in sediments from a hypersaline lake in which such bacteria have been recently discovered. All of the halophilic SOB strains (with the exception of Thiohalomonas nitratireducens) possessed the cbbL gene encoding RuBisCO form I, while the cbbM gene encoding RuBisCO form II was detected only in some of the pure cultures. The general topologies of the CbbL/CbbM trees and the 16S rRNA gene tree were different, but both markers showed that the halophilic SOB genera formed independent lineages in the Gammaproteobacteria. In some cases, such as with several strains of the genus Thiohalospira and with Thioalkalibacter halophilus, the cbbL clustering was incongruent with the positions of these strains on the ribosomal tree. In the cbbM tree, the clustering of Thiohalospira and Thiohalorhabdus strains was incongruent with their branching in both cbbL and 16S rRNA gene trees. cbbL and cbbM genes related to those found in the analysed halophilic SOB were also detected in a sediment from a hypersaline lake in Kulunda Steppe (Russia). Most of the cbbL and cbbM genes belonged to members of the genus Thiohalorhabdus. In the cbbL clone library, sequences related to those of Halothiobacillus and Thiohalospira were detected as minor components. Some of the environmental cbbM sequences belonged to as yet unknown phylotypes, representing deep lineages of halophilic autotrophs.

Hydrogen sulfide degradation characteristics of Bordetella sp. Sulf-8 in a biotrickling filter

The applicability of Bordetella sp. Sulf-8 to degrade Hydrogen Sulfide (H(2)S) gas in a biotrickling system was investigated. The isolate is a heterotrophic gram-negative, catalase- and oxidase-positive, rod-shaped bacterium which can metabolize thiosulfate or sulfide into sulfate. The mesophilic Bordetella sp. Sulf-8 can grow within a wide pH range using yeast as carbon source, with or without the presence of sulfur. In batch experiments, kinetic constants such as maximum specific growth rate (μ (max) = 0.12 1/h), saturation constant (K (S) = 0.017 g/L), and specific sulfur removal rate (88 mg S/g cells h) were obtained. In biotrickling experiments removal efficiencies were satisfactory, but the system performance was observed to be more influenced by empty bed residence time than by H(2)S feed gas concentration. Critical and maximum elimination capacities were 78.0 and 94.5 g H(2)S/m(3) day, respectively. Macrokinetic analysis of the biotrickling system revealed maximum H(2)S removal rate V (max) = 15.97 g S/kg media-day and half saturation constant K (S') = 12.45 ppm(v).

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.

The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments

Many bacteria in the environment have adapted to the presence of toxic heavy metals. Over the last 30 years, this heavy metal tolerance was the subject of extensive research. The bacterium Cupriavidus metallidurans strain CH34, originally isolated by us in 1976 from a metal processing factory, is considered a major model organism in this field because it withstands milli-molar range concentrations of over 20 different heavy metal ions. This tolerance is mostly achieved by rapid ion efflux but also by metal-complexation and -reduction. We present here the full genome sequence of strain CH34 and the manual annotation of all its genes. The genome of C. metallidurans CH34 is composed of two large circular chromosomes CHR1 and CHR2 of, respectively, 3,928,089 bp and 2,580,084 bp, and two megaplasmids pMOL28 and pMOL30 of, respectively, 171,459 bp and 233,720 bp in size. At least 25 loci for heavy-metal resistance (HMR) are distributed over the four replicons. Approximately 67% of the 6,717 coding sequences (CDSs) present in the CH34 genome could be assigned a putative function, and 9.1% (611 genes) appear to be unique to this strain. One out of five proteins is associated with either transport or transcription while the relay of environmental stimuli is governed by more than 600 signal transduction systems. The CH34 genome is most similar to the genomes of other Cupriavidus strains by correspondence between the respective CHR1 replicons but also displays similarity to the genomes of more distantly related species as a result of gene transfer and through the presence of large genomic islands. The presence of at least 57 IS elements and 19 transposons and the ability to take in and express foreign genes indicates a very dynamic and complex genome shaped by evolutionary forces. The genome data show that C. metallidurans CH34 is particularly well equipped to live in extreme conditions and anthropogenic environments that are rich in metals.

Endogenous production of H2S in the gastrointestinal tract: still in search of a physiologic function

Hydrogen sulfide (H(2)S) has long been associated with the gastrointestinal tract, especially the bacteria-derived H(2)S present in flatus. Along with evidence from other organ systems, the finding that gastrointestinal tissues are capable of endogenous production of H(2)S has led to the hypothesis that H(2)S is an endogenous gaseous signaling molecule. In this review, the criteria of gasotransmitters are reexamined, and evidence from the literature regarding H(2)S as a gaseous signaling molecule is discussed. H(2)S is produced enzymatically by gastrointestinal tissues, but evidence is lacking on whether H(2)S production is regulated. H(2)S causes well-defined physiologic effects in gastrointestinal tissues, but evidence for a receptor for H(2)S is lacking. H(2)S is inactivated through enzymatic oxidation, but evidence is lacking on whether manipulating H(2)S oxidation alters endogenous cell signaling. Remaining questions regarding the role of H(2)S as a gaseous signaling molecule in the gastrointestinal tract suggest that H(2)S currently remains a molecule in search of a physiologic function.

Expression of genes for sulfur oxidation in the intracellular chemoautotrophic symbiont of the deep-sea bivalve Calyptogena okutanii

To understand sulfur oxidation in thioauto-trophic deep-sea clam symbionts, we analyzed the recently reported genomes of two chemoautotrophic symbionts of Calyptogena okutanii (Candidatus Vesicomyosocius okutanii strain HA: Vok) and C. magnifica (Candidatus Ruthia magnifica strain Cm: Rma), and examined the sulfur oxidation gene expressions in the Vok by RT-PCR. Both symbionts have genes for sulfide-quinone oxidoreductase (sqr), dissimilatory sulfite reductase (dsr), reversible dissimilatory sulfite reductase (rdsr), sulfur-oxidizing multienzyme system (sox)(soxXYZA and soxB but lacking soxCD), adenosine phosphosulfate reductase (apr), and ATP sulfurylase (sat). While these genomes share 29 orthologous genes for sulfur oxidation implying that both symbionts possess the same sulfur oxidation pathway, Rma has a rhodanese-related sulfurtransferase putative gene (Rmag0316) that has no corresponding ortholog in Vok, and Vok has one unique dsrR (COSY0782). We propose that Calyptogena symbionts oxidize sulfide and thiosulfate, and that sulfur oxidation proceeds as follows. Sulfide is oxidized to sulfite by rdsr. Sulfite is oxidized to sulfate by apr and sat. Thiosulfate is oxidized to zero-valence sulfur by sox, which is then reduced to sulfide by dsr. In addition, thiosulfate may also be oxidized into sulfate by another component of sox. The result of the RT-PCR showed that genes (dsrA, dsrB, dsrC, aprA, aprB, sat, soxB, and sqr) encoding key enzymes catalyzing sulfur oxidation were all equally expressed in the Vok under three different environmental conditions (aerobic, semioxic, and aerobic under high pressure at 9 MPa), indicating that all sulfur oxidation pathways function simultaneously to support intracellular symbiotic life.

Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function

The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14–15,000 Sanger reads per site) was obtained for five high-temperature (>65°C) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O₂ influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H₂-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, Fe, O₂) control microbial community structure and function in YNP geothermal springs.

Structure, function, and evolution of the Thiomonas spp. genome

Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich acid mine drainage (AMD). The genome of one of these strains, Thiomonas sp. 3As, was sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to survive and grow in its highly toxic environment. In order to explore genomic diversity as well as genetic evolution in Thiomonas spp., a comparative genomic hybridization (CGH) approach was used on eight different strains of the Thiomonas genus, including five strains of the same species. Our results suggest that the Thiomonas genome has evolved through the gain or loss of genomic islands and that this evolution is influenced by the specific environmental conditions in which the strains live.

Thiosulfate-dependent chemolithoautotrophic growth of Bradyrhizobium japonicum

Thiosulfate-oxidizing sox gene homologues were found at four loci (I, II, III, and IV) on the genome of Bradyrhizobium japonicum USDA110, a symbiotic nitrogen-fixing bacterium in soil. In fact, B. japonicum USDA110 can oxidize thiosulfate and grow under a chemolithotrophic condition. The deletion mutation of the soxY(1) gene at the sox locus I, homologous to the sulfur-oxidizing (Sox) system in Alphaproteobacteria, left B. japonicum unable to oxidize thiosulfate and grow under chemolithotrophic conditions, whereas the deletion mutation of the soxY(2) gene at sox locus II, homologous to the Sox system in green sulfur bacteria, produced phenotypes similar to those of wild-type USDA110. Thiosulfate-dependent O(2) respiration was observed only in USDA110 and the soxY(2) mutant and not in the soxY(1) mutant. In the cells, 1 mol of thiosulfate was stoichiometrically converted to approximately 2 mol of sulfate and consumed approximately 2 mol of O(2). B. japonicum USDA110 showed (14)CO(2) fixation under chemolithotrophic growth conditions. The CO(2) fixation of resting cells was significantly dependent on thiosulfate addition. These results show that USDA110 is able to grow chemolithoautotrophically using thiosulfate as an electron donor, oxygen as an electron acceptor, and carbon dioxide as a carbon source, which likely depends on sox locus I including the soxY(1) gene on USDA110 genome. Thiosulfate oxidation capability is frequently found in members of the Bradyrhizobiaceae, which phylogenetic analysis showed to be associated with the presence of sox locus I homologues, including the soxY(1) gene of B. japonicum USDA110.

Crystal structure of the electron carrier domain of the reaction center cytochrome c(z) subunit from green photosynthetic bacterium Chlorobium tepidum

In green sulfur photosynthetic bacteria, the cytochrome c(z) (cyt c(z)) subunit in the reaction center complex mediates electron transfer mainly from menaquinol/cytochrome c oxidoreductase to the special pair (P840) of the reaction center. The cyt c(z) subunit consists of an N-terminal transmembrane domain and a C-terminal soluble domain that binds a single heme group. The periplasmic soluble domain has been proposed to be highly mobile and to fluctuate between oxidoreductase and P840 during photosynthetic electron transfer. We have determined the crystal structure of the oxidized form of the C-terminal functional domain of the cyt c(z) subunit (C-cyt c(z)) from thermophilic green sulfur bacterium Chlorobium tepidum at 1.3-A resolution. The overall fold of C-cyt c(z) consists of four alpha-helices and is similar to that of class I cytochrome c proteins despite the low similarity in their amino acid sequences. The N-terminal structure of C-cyt c(z) supports the swinging mechanism previously proposed in relation with electron transfer, and the surface properties provide useful information on possible interaction sites with its electron transfer partners. Several characteristic features are observed for the heme environment: These include orientation of the axial ligands with respect to the heme plane, surface-exposed area of the heme, positions of water molecules, and hydrogen-bond network involving heme propionate groups. These structural features are essential for elucidating the mechanism for regulating the redox state of cyt c(z).

Molecular characterization of inorganic sulfur-compound metabolism in the deep-sea epsilonproteobacterium Sulfurovum sp. NBC37-1

The molecular components involved in energy metabolism of deep-sea Epsilonproteobacteria were characterized in the mesophilic hydrogen- and sulfur-oxidizing chemolithoautotroph Sulfurovum sp. NBC37-1. Previous whole-genome analysis of strain NBC37-1 identified key genes likely to be associated with both sulfur reduction (psr gene families) and oxidation (two sox gene clusters). However, the sox gene clusters showed unique organizations and low homologies to those in other bacteria. Therefore, the biochemical mechanism of inorganic sulfur metabolism has been uncertain. Enzymatic activity measurements and partial protein purification indicated that the Sox enzyme system was constitutively expressed, whereas the expression of sulfur-reduction enzymes varied depending on the culture conditions. The operative Sox system in strain NBC37-1 required membrane components. The molecular basis of energy metabolism reported in this study provides important insight into how deep-sea Epsilonproteobacteria change their energy metabolism in response to variable physical and chemical conditions in mixing zones between hydrothermal fluid and ambient seawater.

Reduced inorganic sulfur oxidation supports autotrophic and mixotrophic growth of Magnetospirillum strain J10 and Magnetospirillum gryphiswaldense

Magnetotactic bacteria are present at the oxic-anoxic transition zone where opposing gradients of oxygen and reduced sulfur and iron exist. Growth of non-magnetotactic lithoautotrophic Magnetospirillum strain J10 and its close relative magnetotactic Magnetospirillum gryphiswaldense was characterized in microaerobic continuous culture. Both strains were able to grow in mixotrophic (acetate + sulfide) and autotrophic (sulfide or thiosulfate) conditions. Autotrophically growing cells completely converted sulfide or thiosulfate to sulfate and produced 7.5 g dry weight per mol substrate at a maximum observed growth rate of 0.09 h(-1) for strain J10 and 0.07 h(-1) for M. gryphiswaldense. The respiratory activity for acetate was repressed in autotrophic and also in mixotrophic cultures, suggesting acetate was used as C-source in the latter. We have estimated the proportions of substrate used for assimilatory processes and evaluated the biomass yields per mol dissimilated substrate. The yield for lithoheterotrophic growth using acetate as the C-source was approximately twice the autotrophic growth yield and very similar to the heterotrophic yield, showing the importance of reduced sulfur compounds for growth. In the draft genome sequence of M. gryphiswaldense homologues of genes encoding a partial sulfur-oxidizing (Sox) enzyme system and reverse dissimilatory sulfite reductase (Dsr) were identified, which may be involved in the oxidation of sulfide and thiosulfate. Magnetospirillum gryphiswaldense is the first freshwater magnetotactic species for which autotrophic growth is shown.

Differential effects of distinct bacterial biofilms in a cave environment

Current microbial surveys using molecular methods provide us with critical information on the major components of natural bacterial communities. However, limited investigation has been performed on the influence of bacterial metabolism on the environment. In this study, we analyzed the pH generated by distinct bacterial communities in a cave environment. Different bacterial biofilms developing on the walls of the cave were visually distinguished by their colorations (e.g., white, yellow, and gray) and mineral depositions, and previous studies have reported on their bacterial diversity and distribution. Using pH microelectrodes, we carried out in situ measurements and were able to detect differences among these bacterial biofilms. White biofilms and carbonate depositions resulted in alkaline pH values. Gray biofilms also increased the pH although these values remained lower than in white biofilms. A combination of gray-white biofilms resulted in alkaline pH values with highest values at the white edge of the colonies. Yellow biofilms generated a slightly acid pH. These results suggest that different bacterial communities can lead to distinct effects on their environment, for instance, precipitation or dissolution of carbonates in caves. These results add information about metabolic response to current knowledge from bacterial diversity surveys, providing information on the interaction between complex bacterial communities and the geological substrate.

Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones

Oxygen minimum zones, also known as oceanic "dead zones," are widespread oceanographic features currently expanding because of global warming. Although inhospitable to metazoan life, they support a cryptic microbiota whose metabolic activities affect nutrient and trace gas cycling within the global ocean. Here, we report metagenomic analyses of a ubiquitous and abundant but uncultivated oxygen minimum zone microbe (SUP05) related to chemoautotrophic gill symbionts of deep-sea clams and mussels. The SUP05 metagenome harbors a versatile repertoire of genes mediating autotrophic carbon assimilation, sulfur oxidation, and nitrate respiration responsive to a wide range of water-column redox states. Our analysis provides a genomic foundation for understanding the ecological and biogeochemical role of pelagic SUP05 in oxygen-deficient oceanic waters and its potential sensitivity to environmental changes.

The speciation of soluble sulphur compounds in bacterial culture fluids by X-ray absorption near edge structure spectroscopy

Over the last decade X-ray absorption near edge structure (XANES) spectroscopy has been used in an increasing number of microbiological studies. In addition to other applications it has served as a valuable tool for the investigation of the sulphur globules deposited intra- or extracellularly by certain photo- and chemotrophic sulphur-oxidizing (Sox) bacteria. For XANES measurements, these deposits can easily be concentrated by filtration or sedimentation through centrifugation. However, during oxidative metabolism of reduced sulphur compounds, such as sulphide or thiosulphate, sulphur deposits are not the only intermediates formed. Soluble intermediates such as sulphite may also be produced and released into the medium. In this study, we explored the potential of XANES spectroscopy for the detection and speciation of sulphur compounds in culture supernatants of the phototrophic purple sulphur bacterium Allochromatium vinosum. More specifically, we investigated A. vinosum DeltasoxY, a strain with an in frame deletion of the soxY gene. This gene encodes an essential component of the thiosulphate-oxidizing Sox enzyme complex. Improved sample preparation techniques developed for the DeltasoxY strain allowed for the first time not only the qualitative but also the quantitative analysis of bacterial culture supernatants by XANES spectroscopy. The results thus obtained verified and supplemented conventional HPLC analysis of soluble sulphur compounds. Sulphite and also oxidized organic sulphur compounds were shown by XANES spectroscopy to be present, some of which were not seen when standard HPLC protocols were used.

Extending the models for iron and sulfur oxidation in the extreme acidophile Acidithiobacillus ferrooxidans

Background

Acidithiobacillus ferrooxidans gains energy from the oxidation of ferrous iron and various reduced inorganic sulfur compounds at very acidic pH. Although an initial model for the electron pathways involved in iron oxidation has been developed, much less is known about the sulfur oxidation in this microorganism. In addition, what has been reported for both iron and sulfur oxidation has been derived from different A. ferrooxidans strains, some of which have not been phylogenetically characterized and some have been shown to be mixed cultures. It is necessary to provide models of iron and sulfur oxidation pathways within one strain of A. ferrooxidans in order to comprehend the full metabolic potential of the pangenome of the genus.

Results

Bioinformatic-based metabolic reconstruction supported by microarray transcript profiling and quantitative RT-PCR analysis predicts the involvement of a number of novel genes involved in iron and sulfur oxidation in A. ferrooxidans ATCC23270. These include for iron oxidation: cup (copper oxidase-like), ctaABT (heme biogenesis and insertion), nuoI and nuoK (NADH complex subunits), sdrA1 (a NADH complex accessory protein) and atpB and atpE (ATP synthetase F0 subunits). The following new genes are predicted to be involved in reduced inorganic sulfur compounds oxidation: a gene cluster (rhd, tusA, dsrE, hdrC, hdrB, hdrA, orf2, hdrC, hdrB) encoding three sulfurtransferases and a heterodisulfide reductase complex, sat potentially encoding an ATP sulfurylase and sdrA2 (an accessory NADH complex subunit). Two different regulatory components are predicted to be involved in the regulation of alternate electron transfer pathways: 1) a gene cluster (ctaRUS) that contains a predicted iron responsive regulator of the Rrf2 family that is hypothesized to regulate cytochrome aa₃ oxidase biogenesis and 2) a two component sensor-regulator of the RegB-RegA family that may respond to the redox state of the quinone pool.

Conclusion

Bioinformatic analysis coupled with gene transcript profiling extends our understanding of the iron and reduced inorganic sulfur compounds oxidation pathways in A. ferrooxidans and suggests mechanisms for their regulation. The models provide unified and coherent descriptions of these processes within the type strain, eliminating previous ambiguity caused by models built from analyses of multiple and divergent strains of this microorganism.

Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB: indications of a surprisingly complex life-style and cryptic anaerobic pathways for aromatic degradation

Background

Initial interest in Dechloromonas aromatica strain RCB arose from its ability to anaerobically degrade benzene. It is also able to reduce perchlorate and oxidize chlorobenzoate, toluene, and xylene, creating interest in using this organism for bioremediation. Little physiological data has been published for this microbe. It is considered to be a free-living organism.

Results

The a priori prediction that the D. aromatica genome would contain previously characterized "central" enzymes to support anaerobic aromatic degradation of benzene proved to be false, suggesting the presence of novel anaerobic aromatic degradation pathways in this species. These missing pathways include the benzylsuccinate synthase (bssABC) genes (responsible for fumarate addition to toluene) and the central benzoyl-CoA pathway for monoaromatics. In depth analyses using existing TIGRfam, COG, and InterPro models, and the creation of de novo HMM models, indicate a highly complex lifestyle with a large number of environmental sensors and signaling pathways, including a relatively large number of GGDEF domain signal receptors and multiple quorum sensors. A number of proteins indicate interactions with an as yet unknown host, as indicated by the presence of predicted cell host remodeling enzymes, effector enzymes, hemolysin-like proteins, adhesins, NO reductase, and both type III and type VI secretory complexes. Evidence of biofilm formation including a proposed exopolysaccharide complex and exosortase (epsH) are also present. Annotation described in this paper also reveals evidence for several metabolic pathways that have yet to be observed experimentally, including a sulphur oxidation (soxFCDYZAXB) gene cluster, Calvin cycle enzymes, and proteins involved in nitrogen fixation in other species (including RubisCo, ribulose-phosphate 3-epimerase, and nif gene families, respectively).

Conclusion

Analysis of the D. aromatica genome indicates there is much to be learned regarding the metabolic capabilities, and life-style, for this microbial species. Examples of recent gene duplication events in signaling as well as dioxygenase clusters are present, indicating selective gene family expansion as a relatively recent event in D. aromatica's evolutionary history. Gene families that constitute metabolic cycles presumed to create D. aromatica's environmental 'foot-print' indicate a high level of diversification between its predicted capabilities and those of its close relatives, A. aromaticum str EbN1 and Azoarcus BH72.

Origin of the Sox multienzyme complex system in ancient thermophilic bacteria and coevolution of its constituent proteins

The multienzyme complex SoxXABYZ(CD)(2), characteristic of facultatively chemolithotrophic Alphaproteobacteria, oxidizes both sulfone and sulfane sulfur species directly to sulfate, while a truncated SoxXABYZ oxidizes only sulfone sulfur in species of Chromatiaceae and Chlorobi. Here we phylogenetically analyzed SoxXA, SoxYZ and SoxCD sequences, correlated the results with earlier SoxB-based data, and postulated that the system originated in putatively common ancestors of Aquificae and Epsilonproteobacteria, and evolved through extensive horizontal gene transfer, accompanied by gain and/or loss of constituents by different lineages. However, in several Sox systems, particularly those from Alphaproteobacteria (and also Chromatiaceae and Chlorobi), there has been no extra gain or loss of constituents and all their proteins have similar evolutionary paths. This implies that the components of these systems have coevolved parallel to each other without any shuffling with other divergent systems. This, however, holds good only for those Sox systems, which render sulfur oxidation functions equivalent to the typical alphaproteobacterial process. We postulate that coevolution of all the proteins is essential for the typical modular function of Sox. Conversely, mosaic Sox systems (where constituents have disparate phylogenetic paths) are either nonfunctional or with activities deviated from typical systems. Monomeric Sox subunits of the mosaic systems, however, possess almost all the motifs and conserved domains critical for their designated activity and heterodimer formation. So what could be the basis of the functional discrepancies of the mosaic Sox systems? It appears that their discretely evolved heterodimers cannot interact among themselves in the same way as ideally envisaged in the modular Sox system, which in turn, may in some cases lead to novel adventitious reactions.

Microbial sulfide oxidation in the oxic-anoxic transition zone of freshwater sediment: involvement of lithoautotrophic Magnetospirillum strain J10

The oxic-anoxic transition zone (OATZ) of freshwater sediments, where opposing gradients exist of reduced iron and sulfide with oxygen, creates a suitable environment for microorganisms that derive energy from the oxidation of iron or sulfide. Gradient microcosms incubated with freshwater sediment showed rapid microbial turnover of sulfide and oxygen compared with sterile systems. Microcosms with FeS as a substrate also showed growth at the OATZ and subsequent dilution series resulted in the isolation of three novel strains, of which strain J10 grows chemolithoautotrophically with reduced sulfur compounds under microaerobic conditions. All three strains are motile spirilla with bipolar flagella, related to the genera Magnetospirillum and Dechlorospirillum within the Alphaproteobacteria. Strain J10 is closely related to Magnetospirillum gryphiswaldense and is the first strain in this genus found to be capable of autotrophic growth. Thiosulfate was oxidized completely to sulfate, with a yield of 4 g protein mol(-1) thiosulfate, and autotrophic growth was evidenced by incorporation of (13)C derived from bicarbonate into biomass. A putative gene encoding ribulose 1,5-bisphosphate carboxylase/oxygenase type II was identified in strain J10, suggesting that the Calvin-Benson-Bassham cycle is used for autotrophic growth. Analogous genes are also present in other magnetospirilla, and in the autotrophically growing alphaproteobacterium magnetic vibrio MV-1.

Mechanism for the hydrolysis of a sulfur-sulfur bond based on the crystal structure of the thiosulfohydrolase SoxB

SoxB is an essential component of the bacterial Sox sulfur oxidation pathway. SoxB contains a di-manganese(II) site and is proposed to catalyze the release of sulfate from a protein-bound cysteine S-thiosulfonate. A direct assay for SoxB activity is described. The structure of recombinant Thermus thermophilus SoxB was determined by x-ray crystallography to a resolution of 1.5 A. Structures were also determined for SoxB in complex with the substrate analogue thiosulfate and in complex with the product sulfate. A mechanistic model for SoxB is proposed based on these structures.

Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea

Lithotrophic sulfur oxidation is an ancient metabolic process. Ecologically and taxonomically diverged prokaryotes have differential abilities to utilize different reduced sulfur compounds as lithotrophic substrates. Different phototrophic or chemotrophic species use different enzymes, pathways and mechanisms of electron transport and energy conservation for the oxidation of any given substrate. While the mechanisms of sulfur oxidation in obligately chemolithotrophic bacteria, predominantly belonging to Beta- (e.g. Thiobacillus) and Gammaproteobacteria (e.g. Thiomicrospira), are not well established, the Sox system is the central pathway in the facultative bacteria from Alphaproteobacteria (e.g. Paracoccus). Interestingly, photolithotrophs such as Rhodovulum belonging to Alphaproteobacteria also use the Sox system, whereas those from Chromatiaceae and Chlorobi use a truncated Sox complex alongside reverse-acting sulfate-reducing systems. Certain chemotrophic magnetotactic Alphaproteobacteria allegedly utilize such a combined mechanism. Sulfur-chemolithotrophic metabolism in Archaea, largely restricted to Sulfolobales, is distinct from those in Bacteria. Phylogenetic and biomolecular fossil data suggest that the ubiquity of sox genes could be due to horizontal transfer, and coupled sulfate reduction/sulfide oxidation pathways, originating in planktonic ancestors of Chromatiaceae or Chlorobi, could be ancestral to all sulfur-lithotrophic processes. However, the possibility that chemolithotrophy, originating in deep sea, is the actual ancestral form of sulfur oxidation cannot be ruled out.

Complete genome sequence of the chemolithoautotrophic marine magnetotactic coccus strain MC-1

The marine bacterium strain MC-1 is a member of the alpha subgroup of the proteobacteria that contains the magnetotactic cocci and was the first member of this group to be cultured axenically. The magnetotactic cocci are not closely related to any other known alphaproteobacteria and are only distantly related to other magnetotactic bacteria. The genome of MC-1 contains an extensive (102 kb) magnetosome island that includes numerous genes that are conserved among all known magnetotactic bacteria, as well as some genes that are unique. Interestingly, certain genes that encode proteins considered to be important in magnetosome assembly (mamJ and mamW) are absent from the genome of MC-1. Magnetotactic cocci exhibit polar magneto-aerotaxis, and the MC-1 genome contains a relatively large number of identified chemotaxis genes. Although MC-1 is capable of both autotrophic and heterotrophic growth, it does not appear to be metabolically versatile, with heterotrophic growth confined to the utilization of acetate. Central carbon metabolism is encoded by genes for the citric acid cycle (oxidative and reductive), glycolysis, and gluconeogenesis. The genome also reveals the presence or absence of specific genes involved in the nitrogen, sulfur, iron, and phosphate metabolism of MC-1, allowing us to infer the presence or absence of specific biochemical pathways in strain MC-1. The pathways inferred from the MC-1 genome provide important information regarding central metabolism in this strain that could provide insights useful for the isolation and cultivation of new magnetotactic bacterial strains, in particular strains of other magnetotactic cocci.

Sulfur Oxygenase Reductase in Different Acidithiobacillus Caldus-Like Strains

The elemental sulfur oxidising enzyme Sulfur Oxygenase Reductase (SOR) is very well investigated in acidothermophilic archaea, such as Acidianus brierleyi and Sulfolobus metallicus. In contrast, not much is known about the biochemistry of elemental sulfur oxidation in acidophilic bacteria. Recently, however, the SOR-encoding gene has been found also in a bacterial strain closely related to the moderate thermophile Acidithiobacillus caldus. Confusingly, for the latter species, also the involvement of the SOX system as well as thiosulfate:quinone oxidoreductase (TQO) and tetrathionate hydrolase (TTH) in sulfur compound oxidation has been proposed based on genome analysis. In this study, we have detected the sor-gene in other Acidithiobacillus caldus-like strains, isolated from various bioleaching habitats, indicating that SOR plays an important role in sulfur oxidation in this species. Based on sequence comparison, the new bacterial sor-genes are closely related and distant from the known archaeal sequences as well as from the SOR found in the neutrophilic bacterium Aquifex aeolicus. In addition, SOR activity has been detected in crude cell extracts from all Acidithiobacillus caldus-like strains tested. The enzyme is truly thermophilic as highest activities were achieved at 65 °C, which is far beyond the growth optimum of Acidithiobacillus caldus. This finding may give rise to the question whether the presence of SOR in Acidithiobacillus caldus is only relevant while growing at elevated temperatures. Currently, experiments are performed for testing this hypothesis (comparing growth and enzyme activities at 30 vs. 45 °C).

Sigma factor mimicry involved in regulation of general stress response

Bacteria have evolved regulatory traits to rapidly adapt to changing conditions. Two principal regulatory mechanisms to modulate gene expression consist of regulation via alternative sigma factors and phosphorylation-dependent response regulators. PhyR represents a recently discovered protein family combining parts of both systems: a sigma factor-like domain of the extracytoplasmic function (ECF) subfamily linked to a receiver domain of a response regulator. Here we investigated the mode of action of this key regulator of general stress response in Methylobacterium extorquens. Our results indicate that PhyR does not act as a genuine sigma factor but instead controls gene expression indirectly through protein-protein interactions. This is evident from the analysis of additional proteins involved in PhyR-dependent gene regulation. We demonstrated that the ECF sigma factor-like domain of PhyR interacts with a protein, designated NepR, upon phosphorylation of the PhyR receiver domain. Using transcriptome analysis and phenotypic assays, we showed that NepR is a negative regulator of PhyR response. Furthermore, we provide biochemical and genetic evidence that NepR exerts this inhibitory effect through sequestration of the ECF sigma factor sigma(EcfG1). Our data support an unprecedented model according to which PhyR acts as a mimicry protein triggering a partner-switching mechanism. Such a regulation of general stress response clearly differs from the two known models operating via sigma(S) and sigma(B). Given the absence of these master regulators and the concomitant conservation of PhyR in Alphaproteobacteria, the novel mechanism presented here is most likely central to the control of general stress response in this large subclass of Proteobacteria.

Thiosulfate oxidation by Comamonas sp. S23 isolated from a sulfur spring

A bacterial isolate S23 capable of oxidizing thiosulfate was isolated from a sulfur spring. Strain S23 is gram-negative, aerobic, and motile. The G + C content of DNA is 61.4 mol%. The fatty acid composition and phylogenetic analysis of the 16S rRNA gene sequence of strain S23 showed that it is related to the members of the genus Comamonas, and most closely related to Comamonas testosteroni (99.9% sequence similarity). The isolate S23 exhibited thiosulfate oxidation under a mixotrophic growth condition. Polymerase chain reaction (PCR) using soxB-specific primers and DNA sequencing showed the presence of the soxB gene. This is the first report in Comamonas sp. showing thiosulfate oxidation under a mixotrophic growth condition.

Genetic polymorphism at the candidate gene in Iranian Sistani cattle (Bos indicus)

The genotypes for Leptin, Kappa-Casein, Calpastatin and BoLA-DRB3 loci were determined by polymerase chain reaction and restriction enzyme digestion method in native Iranian breed cattle, Sistani. Blood samples were collected from Sistani Breeding Station located in Zehak, Zabol in Iran. The extraction of genomic DNA was based on Guanidin Thiocyanate-Silica gel method. After PCR reaction, amplicons were digested with appropriate restriction enzymes. The Calpastatin locus had 3 genotypes with frequencies of 0.62, 0.29 and 0.09 for MM, MN and NN, respectively; kappa-Casein and Leptin had 3 genotypes with frequencies of 0.27, 0.57 and 0.16 for kappa-Casein, 0.77, 0.22 and 0.01 for Leptin for AA, AB and BB genotypes, respectively. For BoLA-DRB3 we identified 19 alleles, that DRB3. 2*8 had the highest allelic frequency (22.4%) and DRB3. 2*3, *29, *37 and *51 had the lowest allelic frequency (1%). One of the 19 alleles had a new pattern. Average heterozygosity values for all loci were low. Chi2-test did not confirm the Hardy-Weinberg equilibrium for Leptin and Calpastatin in this population. These data provide evidence that Iranian's Sistani breed have a good genetic variability, which opens interesting prospects for future selection programs, especially marker-assistant selection.

Sulfur metabolism in phototrophic sulfur bacteria

Phototrophic sulfur bacteria are characterized by oxidizing various inorganic sulfur compounds for use as electron donors in carbon dioxide fixation during anoxygenic photosynthetic growth. These bacteria are divided into the purple sulfur bacteria (PSB) and the green sulfur bacteria (GSB). They utilize various combinations of sulfide, elemental sulfur, and thiosulfate and sometimes also ferrous iron and hydrogen as electron donors. This review focuses on the dissimilatory and assimilatory metabolism of inorganic sulfur compounds in these bacteria and also briefly discusses these metabolisms in other types of anoxygenic phototrophic bacteria. The biochemistry and genetics of sulfur compound oxidation in PSB and GSB are described in detail. A variety of enzymes catalyzing sulfur oxidation reactions have been isolated from GSB and PSB (especially Allochromatium vinosum, a representative of the Chromatiaceae), and many are well characterized also on a molecular genetic level. Complete genome sequence data are currently available for 10 strains of GSB and for one strain of PSB. We present here a genome-based survey of the distribution and phylogenies of genes involved in oxidation of sulfur compounds in these strains. It is evident from biochemical and genetic analyses that the dissimilatory sulfur metabolism of these organisms is very complex and incompletely understood. This metabolism is modular in the sense that individual steps in the metabolism may be performed by different enzymes in different organisms. Despite the distant evolutionary relationship between GSB and PSB, their photosynthetic nature and their dependency on oxidation of sulfur compounds resulted in similar ecological roles in the sulfur cycle as important anaerobic oxidizers of sulfur compounds.

Investigation of elemental sulfur speciation transformation mediated by Acidithiobacillus ferrooxidans

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.

Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications

BACKGROUND

Acidithiobacillus ferrooxidans is a major participant in consortia of microorganisms used for the industrial recovery of copper (bioleaching or biomining). It is a chemolithoautrophic, gamma-proteobacterium using energy from the oxidation of iron- and sulfur-containing minerals for growth. It thrives at extremely low pH (pH 1-2) and fixes both carbon and nitrogen from the atmosphere. It solubilizes copper and other metals from rocks and plays an important role in nutrient and metal biogeochemical cycling in acid environments. The lack of a well-developed system for genetic manipulation has prevented thorough exploration of its physiology. Also, confusion has been caused by prior metabolic models constructed based upon the examination of multiple, and sometimes distantly related, strains of the microorganism.

RESULTS

The genome of the type strain A. ferrooxidans ATCC 23270 was sequenced and annotated to identify general features and provide a framework for in silico metabolic reconstruction. Earlier models of iron and sulfur oxidation, biofilm formation, quorum sensing, inorganic ion uptake, and amino acid metabolism are confirmed and extended. Initial models are presented for central carbon metabolism, anaerobic metabolism (including sulfur reduction, hydrogen metabolism and nitrogen fixation), stress responses, DNA repair, and metal and toxic compound fluxes.

CONCLUSION

Bioinformatics analysis provides a valuable platform for gene discovery and functional prediction that helps explain the activity of A. ferrooxidans in industrial bioleaching and its role as a primary producer in acidic environments. An analysis of the genome of the type strain provides a coherent view of its gene content and metabolic potential.

Functional analysis of three sulfide:quinone oxidoreductase homologs in Chlorobaculum tepidum

Sulfide:quinone oxidoreductase (SQR) catalyzes sulfide oxidation during sulfide-dependent chemo- and phototrophic growth in bacteria. The green sulfur bacterium Chlorobaculum tepidum (formerly Chlorobium tepidum) can grow on sulfide as the sole electron donor and sulfur source. C. tepidum contains genes encoding three SQR homologs: CT0117, CT0876, and CT1087. This study examined which, if any, of the SQR homologs possess sulfide-dependent ubiquinone reduction activity and are required for growth on sulfide. In contrast to CT0117 and CT0876, transcripts of CT1087 were detected only when cells actively oxidized sulfide. Mutation of CT0117 or CT1087 in C. tepidum decreased SQR activity in membrane fractions, and the CT1087 mutant could not grow with >or=6 mM sulfide. Mutation of both CT0117 and CT1087 in C. tepidum completely abolished SQR activity, and the double mutant failed to grow with >or=4 mM sulfide. A C-terminal His(6)-tagged CT1087 protein was membrane localized, as was SQR activity. Epitope-tagged CT1087 was detected only when sulfide was actively consumed by cells. Recombinantly produced CT1087 and CT0117 proteins had SQR activity, while CT0876 did not. In summary, we conclude that, under the conditions tested, both CT0117 and CT1087 function as SQR proteins in C. tepidum. CT0876 may support the growth of C. tepidum at low sulfide concentrations, but no evidence was found for SQR activity associated with this protein.

Identification of two inactive forms of the central sulfur cycle protein SoxYZ of Paracoccus pantotrophus

The central protein of the sulfur-oxidizing enzyme system of Paracoccus pantotrophus, SoxYZ, reacts with three different Sox proteins. Its active site Cys110(Y) is on the carboxy-terminus of the SoxY subunit. SoxYZ "as isolated" consisted mainly of the catalytically inactive SoxY-Y(Z)(2) heterotetramer linked by a Cys110(Y)-Cys110(Y) interprotein disulfide. Sulfide activated SoxYZ "as isolated" 456-fold, reduced the disulfide, and yielded an active SoxYZ heterodimer. The reductant tris(2-carboxyethyl)phosphine (TCEP) inactivated SoxYZ. This form was not re-activated by sulfide, which identified it as a different inactive form. In analytical gel filtration, the elution of "TCEP-treated" SoxYZ was retarded compared to active SoxYZ, indicating a conformational change. The possible enzymes involved in the re-activation of each inactive form of SoxYZ are discussed.

Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotes

Sulfur-oxidizing prokaryotes (SOP) catalyse a central step in the global S-cycle and are of major functional importance for a variety of natural and engineered systems, but our knowledge on their actual diversity and environmental distribution patterns is still rather limited. In this study we developed a specific PCR assay for the detection of dsrAB that encode the reversely operating sirohaem dissimilatory sulfite reductase (rDSR) and are present in many but not all published genomes of SOP. The PCR assay was used to screen 42 strains of SOP (most without published genome sequence) representing the recognized diversity of this guild. For 13 of these strains dsrAB was detected and the respective PCR product was sequenced. Interestingly, most dsrAB-encoding SOP are capable of forming sulfur storage compounds. Phylogenetic analysis demonstrated largely congruent rDSR and 16S rRNA consensus tree topologies, indicating that lateral transfer events did not play an important role in the evolutionary history of known rDSR. Thus, this enzyme represents a suitable phylogenetic marker for diversity analyses of sulfur storage compound-exploiting SOP in the environment. The potential of this new functional gene approach was demonstrated by comparative sequence analyses of all dsrAB present in published metagenomes and by applying it for a SOP census in selected marine worms and an alkaline lake sediment.

Sulfur oxidation of Paracoccus pantotrophus: the sulfur-binding protein SoxYZ is the target of the periplasmic thiol-disulfide oxidoreductase SoxS

The periplasmic thiol-disulfide oxidoreductase SoxS is essential for chemotrophic growth of Paracoccus pantotrophus with thiosulfate. To trap its periplasmic partner, the cysteine residues of the CysXaaXaaCys motif of SoxS (11 kDa) were changed to alanine by site-directed mutagenesis. The disrupted soxS gene of the homogenote mutant G OmegaS was complemented with plasmids carrying the mutated soxS[C13A] or soxS[C16A] gene. Strain G OmegaS(pRD179.6[C16A](S)) displayed a marginal thiosulfate-oxidizing activity, suggesting that Cys13(S) binds the target protein. Evidence is presented that SoxS specifically binds SoxY. (i) Immunoblot analysis using non-reducing SDS gel electrophoresis and anti-SoxS and anti-SoxYZ antibodies identified the respective antigens of strain G OmegaS(pRD179.6[C16A](S)) at the 25 kDa position, suggesting an adduct of about 14 kDa, close to the value expected for SoxY migration. (ii) A mutant unable to produce SoxYZ, such as strain G OmegaX(pRD187.7[C16A](S)), did not form a SoxS(C16A) adduct, while addition of homogeneous SoxYZ resulted in the 25 kDa adduct. (iii) The SoxY and SoxZ subunits were distinguished by site-directed mutagenesis of the cysteine residue in SoxZ. SoxYZ(C53S) formed the 25 kDa adduct with SoxS(C16A). These results demonstrate that the target of SoxS is the sulfur-binding protein SoxY of the SoxYZ complex. As SoxYZ is reversibly inactivated, SoxS may activate SoxYZ as a crucial function for chemotrophy of P. pantotrophus.

X-ray absorption spectroscopy as a probe of microbial sulfur biochemistry: the nature of bacterial sulfur globules revisited

The chemical nature of the sulfur in bacterial sulfur globules has been the subject of controversy for a number of years. Sulfur K-edge X-ray absorption spectroscopy (XAS) is a powerful technique for probing the chemical forms of sulfur in situ, but two groups have used it with very different conclusions. The root of the controversy lies with the different detection strategies used by the two groups, which result in very different spectra. This paper seeks to resolve the controversy. We experimentally demonstrate that the use of transmittance detection for sulfur K-edge XAS measurements is highly prone to spectroscopic distortions and that much of the published work on sulfur bacteria is very likely based on distorted data. We also demonstrate that all three detection methods used for X-ray absorption experiments yield essentially identical spectra when the measurements are carried out under conditions where no experimental distortions are expected. Finally, we turn to the original question--the chemical nature of bacterial sulfur. We examine isolated sulfur globules of Allochromatium vinosum and intact cells of a strain of magnetotactic coccus and show that XAS indicates the presence of a chemical form of sulfur resembling S(8).

SoxAX binding protein, a novel component of the thiosulfate-oxidizing multienzyme system in the green sulfur bacterium Chlorobium tepidum

From the photosynthetic green sulfur bacterium Chlorobium tepidum (pro synon. Chlorobaculum tepidum), we have purified three factors indispensable for the thiosulfate-dependent reduction of the small, monoheme cytochrome c(554). These are homologues of sulfur-oxidizing (Sox) system factors found in various thiosulfate-oxidizing bacteria. The first factor is SoxYZ that serves as the acceptor for the reaction intermediates. The second factor is monomeric SoxB that is proposed to catalyze the hydrolytic cleavage of sulfate from the SoxYZ-bound oxidized product of thiosulfate. The third factor is the trimeric cytochrome c(551), composed of the monoheme cytochrome SoxA, the monoheme cytochrome SoxX, and the product of the hypothetical open reading frame CT1020. The last three components were expressed separately in Escherichia coli cells and purified to homogeneity. In the presence of the other two Sox factors, the recombinant SoxA and SoxX showed a low but discernible thiosulfate-dependent cytochrome c(554) reduction activity. The further addition of the recombinant CT1020 protein greatly increased the activity, and the total activity was as high as that of the native SoxAX-CT1020 protein complex. The recombinant CT1020 protein participated in the formation of a tight complex with SoxA and SoxX and will be referred to as SAXB (SoxAX binding protein). Homologues of the SAXB gene are found in many strains, comprising roughly about one-third of the thiosulfate-oxidizing bacteria whose sox gene cluster sequences have been deposited so far and ranging over the Chlorobiaciae, Chromatiaceae, Hydrogenophilaceae, Oceanospirillaceae, etc. Each of the deduced SoxA and SoxX proteins of these bacteria constitute groups that are distinct from those found in bacteria that apparently lack SAXB gene homologues.

SoxAX cytochromes, a new type of heme copper protein involved in bacterial energy generation from sulfur compounds

SoxAX cytochromes are essential for the function of the only confirmed pathway for bacterial thiosulfate oxidation, the so-called "Sox pathway," in which they catalyze the initial formation of a S-S bond between thiosulfate and the SoxYZ carrier protein. Our work using the Starkeya novella diheme SoxAX protein reveals for the first time that in addition to two active site heme groups, SoxAX contains a mononuclear Cu(II) center with a distorted tetragonal geometry and three to four nitrogen ligands, one of which is a histidine. The Cu(II) center enhanced SoxAX activity in a newly developed, glutathione-based assay system that mimics the natural reaction of SoxAX with SoxYZ. EPR spectroscopy confirmed that the SoxAX Cu(II) center is reduced by glutathione. At pH 7 a K(m) (app) of 0.19+/-0.028 mm and a k(cat) (app) of 5.7+/-0.25s(-1) were determined for glutathione. We propose that SoxAX cytochromes are a new type of heme-copper proteins, with SoxAX-mediated S-S bond formation involving both the copper and heme centers.

Variability in Halothiobacillus neapolitanus type strain cultures

Numerous microbial species are reported to utilize oxidation and/or reduction of sulfur containing compounds in the energy producing portions of their metabolism Halothiobacillus neapolitanus cultures obtained from different commercial sources appear to display considerable variability in terms of growth rate, carbonate consumption and activity of individual enzymes.

Genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1

Microbial Mn(II) oxidation has important biogeochemical consequences in marine, freshwater, and terrestrial environments, but many aspects of the physiology and biochemistry of this process remain obscure. Here, we report genomic insights into Mn(II) oxidation by the marine alphaproteobacterium Aurantimonas sp. strain SI85-9A1, isolated from the oxic/anoxic interface of a stratified fjord. The SI85-9A1 genome harbors the genetic potential for metabolic versatility, with genes for organoheterotrophy, methylotrophy, oxidation of sulfur and carbon monoxide, the ability to grow over a wide range of O(2) concentrations (including microaerobic conditions), and the complete Calvin cycle for carbon fixation. Although no growth could be detected under autotrophic conditions with Mn(II) as the sole electron donor, cultures of SI85-9A1 grown on glycerol are dramatically stimulated by addition of Mn(II), suggesting an energetic benefit from Mn(II) oxidation. A putative Mn(II) oxidase is encoded by duplicated multicopper oxidase genes that have a complex evolutionary history including multiple gene duplication, loss, and ancient horizontal transfer events. The Mn(II) oxidase was most abundant in the extracellular fraction, where it cooccurs with a putative hemolysin-type Ca(2+)-binding peroxidase. Regulatory elements governing the cellular response to Fe and Mn concentration were identified, and 39 targets of these regulators were detected. The putative Mn(II) oxidase genes were not among the predicted targets, indicating that regulation of Mn(II) oxidation is controlled by other factors yet to be identified. Overall, our results provide novel insights into the physiology and biochemistry of Mn(II) oxidation and reveal a genome specialized for life at the oxic/anoxic interface.

Complete genome sequence of Nitrobacter hamburgensis X14 and comparative genomic analysis of species within the genus Nitrobacter

The alphaproteobacterium Nitrobacter hamburgensis X14 is a gram-negative facultative chemolithoautotroph that conserves energy from the oxidation of nitrite to nitrate. Sequencing and analysis of the Nitrobacter hamburgensis X14 genome revealed four replicons comprised of one chromosome (4.4 Mbp) and three plasmids (294, 188, and 121 kbp). Over 20% of the genome is composed of pseudogenes and paralogs. Whole-genome comparisons were conducted between N. hamburgensis and the finished and draft genome sequences of Nitrobacter winogradskyi and Nitrobacter sp. strain Nb-311A, respectively. Most of the plasmid-borne genes were unique to N. hamburgensis and encode a variety of functions (central metabolism, energy conservation, conjugation, and heavy metal resistance), yet approximately 21 kb of a approximately 28-kb "autotrophic" island on the largest plasmid was conserved in the chromosomes of Nitrobacter winogradskyi Nb-255 and Nitrobacter sp. strain Nb-311A. The N. hamburgensis chromosome also harbors many unique genes, including those for heme-copper oxidases, cytochrome b(561), and putative pathways for the catabolism of aromatic, organic, and one-carbon compounds, which help verify and extend its mixotrophic potential. A Nitrobacter "subcore" genome was also constructed by removing homologs found in strains of the closest evolutionary relatives, Bradyrhizobium japonicum and Rhodopseudomonas palustris. Among the Nitrobacter subcore inventory (116 genes), copies of genes or gene clusters for nitrite oxidoreductase (NXR), cytochromes associated with a dissimilatory nitrite reductase (NirK), PII-like regulators, and polysaccharide formation were identified. Many of the subcore genes have diverged significantly from, or have origins outside, the alphaproteobacterial lineage and may indicate some of the unique genetic requirements for nitrite oxidation in Nitrobacter.