Tn5-induced mutations affecting sulfur-oxidizing ability (Sox) of Thiosphaera pantotropha

Complete Genome Sequence and Annotation of the Paracoccus pantotrophus Type Strain DSM 2944

Paracoccus spp. are metabolically versatile alphaproteobacteria able to perform heterotrophic and chemoautotrophic growth. This study describes the whole-genome sequence of the Paracoccus pantotrophus type strain DSM 2944 (ATCC 35512, LMD 82.5, GB17). The genome sequence revealed the presence of a complete phaZ phaC phaP phaR gene cluster related to polyhydroxyalkanoate metabolism.

Paracoccus spp. are metabolically versatile alphaproteobacteria able to perform heterotrophic and chemoautotrophic growth. This study describes the whole-genome sequence of the Paracoccus pantotrophus type strain DSM 2944 (ATCC 35512, LMD 82.5, GB17). The genome sequence revealed the presence of a complete phaZ phaC phaP phaR gene cluster related to polyhydroxyalkanoate metabolism.

Metabolic adaptation and trophic strategies of soil bacteria-C1- metabolism and sulfur chemolithotrophy in Starkeya novella

The highly diverse and metabolically versatile microbial communities found in soil environments are major contributors to the global carbon, nitrogen, and sulfur cycles. We have used a combination of genome -based pathway analysis with proteomics and gene expression studies to investigate metabolic adaptation in a representative of these bacteria, Starkeya novella, which was originally isolated from agricultural soil. This bacterium was the first facultative sulfur chemolithoautotroph that was isolated and it is also able to grow with methanol and on over 39 substrates as a heterotroph. However, using glucose, fructose, methanol, thiosulfate as well as combinations of the carbon compounds with thiosulfate as growth substrates we have demonstrated here that contrary to the previous classification, S. novella is not a facultative sulfur chemolitho- and methylotroph, as the enzyme systems required for these two growth modes are always expressed at high levels. This is typical for key metabolic pathways. In addition enzymes for various pathways of carbon dioxide fixation were always expressed at high levels, even during heterotrophic growth on glucose or fructose, which suggests a role for these pathways beyond the generation of reduced carbon units for cell growth, possibly in redox balancing of metabolism. Our results then indicate that S. novella, a representative of the Xanthobacteraceae family of methylotrophic soil and freshwater dwelling bacteria, employs a mixotrophic growth strategy under all conditions tested here. As a result the contribution of this bacterium to either carbon sequestration or the release of climate active substances could vary very quickly, which has direct implications for the modeling of such processes if mixotrophy proves to be the main growth strategy for large populations of soil bacteria.

Regulation of dissimilatory sulfur oxidation in the purple sulfur bacterium allochromatium vinosum

In the purple sulfur bacterium Allochromatium vinosum, thiosulfate oxidation is strictly dependent on the presence of three periplasmic Sox proteins encoded by the soxBXAK and soxYZ genes. It is also well documented that proteins encoded in the dissimilatory sulfite reductase (dsr) operon, dsrABEFHCMKLJOPNRS, are essential for the oxidation of sulfur that is stored intracellularly as an obligatory intermediate during the oxidation of thiosulfate and sulfide. Until recently, detailed knowledge about the regulation of the sox genes was not available. We started to fill this gap and show that these genes are expressed on a low constitutive level in A. vinosum in the absence of reduced sulfur compounds. Thiosulfate and possibly sulfide lead to an induction of sox gene transcription. Additional translational regulation was not apparent. Regulation of soxXAK is probably performed by a two-component system consisting of a multi-sensor histidine kinase and a regulator with proposed di-guanylate cyclase activity. Previous work already provided some information about regulation of the dsr genes encoding the second important sulfur-oxidizing enzyme system in the purple sulfur bacterium. The expression of most dsr genes was found to be at a low basal level in the absence of reduced sulfur compounds and enhanced in the presence of sulfide. In the present work, we focused on the role of DsrS, a protein encoded by the last gene of the dsr locus in A. vinosum. Transcriptional and translational gene fusion experiments suggest a participation of DsrS in the post-transcriptional control of the dsr operon. Characterization of an A. vinosum ΔdsrS mutant showed that the monomeric cytoplasmic 41.1-kDa protein DsrS is important though not essential for the oxidation of sulfur stored in the intracellular sulfur globules.

Redefining Paracoccus denitrificans and Paracoccus pantotrophus and the case for a reassessment of the strains held by international culture collections

An outline of the current taxonomic diversity of the genus Paracoccus is presented. A definitive summary is given of the valid type strains of Paracoccus denitrificans and Paracoccus pantotrophus and of culture collection strains that can be assigned to these species. The case is established for a critical reassessment of the P. denitrificans strains held by international culture collections, to ensure that they are assigned to the correct species.

The flavoprotein SoxF functions in chemotrophic thiosulfate oxidation of Paracoccus pantotrophus in vivo and in vitro

Paracoccus pantotrophus strain GBsoxFDelta carries a deletion in the soxF gene that inactivates flavoprotein SoxF-sulfide dehydrogenase. This strain grew with thiosulfate slower than the wild type. GBsoxFDelta cells oxidized thiosulfate at a rate of 40% and hydrogen sulfide at a rate of 45% of the wild type. Complementation of GBsoxFDelta with plasmid pRIsoxF carrying the soxF gene increased these rates to 83% and 70%, respectively. However, GBsoxFDelta and GBsoxFDelta (pRIsoxF) oxidized thiosulfate and hydrogen sulfide to sulfate as evident from the yield of electrons. The thiosulfate oxidation rate of cell-free extracts of strain GBsoxFDelta was increased when supplemented with SoxF isolated from the wild type. However, SoxF did not affect the thiosulfate-oxidizing activity of the Sox enzyme system as reconstituted from the 'as-isolated' four Sox proteins. These data demonstrated that SoxF enhanced chemotrophic thiosulfate oxidation in vivo and acted on some component or condition present in whole cells and cell-free extracts but not present in the reconstituted system.

SoxV transfers electrons to the periplasm of Paracoccus pantotrophus - an essential reaction for chemotrophic sulfur oxidation

The soxVW genes are located upstream of the sox gene cluster encoding the sulfur-oxidizing ability of Paracoccus pantotrophus. SoxV is highly homologous to CcdA, which is involved in cytochrome c maturation of P. pantotrophus. SoxV was shown to function in reduction of the periplasmic SoxW, which shows a CysXaaXaaCys motif characteristic for thioredoxins. From strain GBOmegaV, which carries an Omega-kanamycin-resistance-encoding interposon in soxV, and complementation analysis it was evident that SoxV but not the periplasmic SoxW was essential for lithoautotrophic growth of P. pantotrophus with thiosulfate. However, the thiosulfate-oxidizing activities of cell extracts from the wild-type and from strain GBOmegaV were similar, demonstrating that the low thiosulfate-oxidizing activity of strain GBOmegaV in vivo was not due to a defect in biosynthesis or maturation of proteins of the Sox system and suggesting that SoxV is part of a regulatory or catalytic system of the Sox system. Analysis of DNA sequences available from different organisms harbouring a Sox system revealed that soxVW genes are exclusively present in sox operons harbouring the soxCD genes, encoding sulfur dehydrogenase, suggesting that SoxCD might be a redox partner of SoxV. No complementation of the ccdA mutant P. pantotrophus TP43 defective in cytochrome c maturation was achieved by expression of soxV in trans, demonstrating that the high identity of SoxV and CcdA does not correspond to functional homology.

SoxRS-mediated regulation of chemotrophic sulfur oxidation in Paracoccus pantotrophus

Paracoccus pantotrophus GB17 requires thiosulfate for induction of the sulfur-oxidizing (Sox) enzyme system. The soxRS genes are divergently oriented to the soxVWXYZA–H genes. soxR predicts a transcriptional regulator of the ArsR family and soxS a periplasmic thioredoxin. The homogenote mutant GBΩS carrying a disruption of soxS by the Ω-kanamycin-resistance-encoding interposon expressed a low thiosulfate-oxidizing activity under heterotrophic and mixotrophic growth conditions. This activity was repressed by complementation with soxR, suggesting that SoxR acts as a repressor and SoxS is essential for full expression. Sequence analysis uncovered operator characteristics in the intergenic regions soxS–soxV and soxW–soxX. In each region a transcription start site was identified by primer extension analysis. Both regions were cloned into the vector pRI1 and transferred to P. pantotrophus. Strains harbouring pRI1 with soxS–soxV or soxW–soxX expressed the sox genes under heterotrophic conditions at a low rate, indicating repressor titration. Sequence analysis of SoxR suggested a helix–turn–helix (HTH) motif at position 87–108 and uncovered an invariant Cys-80 and a cysteine residue at the C-terminus. SoxR was overproduced in Escherichia coli with an N-terminal His6-tag and purified to near homogeneity. Electrophoretic gel mobility shift assays with SoxR retarded the soxS–soxV region as a single band while the soxW–soxX region revealed at least two protein–DNA complexes. These data demonstrated binding of SoxR to the relevant DNA. This is believed to be the first report of regulation of chemotrophic sulfur oxidation at the molecular level.

Sulfide dehydrogenase activity of the monomeric flavoprotein SoxF of Paracoccus pantotrophus

Flavocytochrome c-sulfide dehydrogenases (FCSDs) are complexes of a flavoprotein with a c-type cytochrome performing hydrogen sulfide-dependent cytochrome c reduction in vitro. The amino acid sequence analysis revealed that the phylogenetic relationship of different flavoproteins reflected the relationship of sulfur-oxidizing bacteria. The flavoprotein SoxF of Paracoccus pantotrophus is 29-67% identical to the flavoprotein subunit of FCSD of phototrophic sulfur-oxidizing bacteria. Purification of SoxF yielded a homogeneous emerald-green monomeric protein of 42 797 Da. SoxF catalyzed sulfide-dependent horse heart cytochrome c reduction at the optimum pH of 6.0 with a k(cat) of 3.9 s(-1), a K(m) of 2.3 microM for sulfide, and a K(m) of 116 microM for cytochrome c, as determined by nonlinear regression analysis. The yield of 1.9 mol of cytochrome c reduced per mole of sulfide suggests sulfur or polysulfide as the product. Sulfide dehydrogenase activity of SoxF was inhibited by sulfur (K(i) = 1.3 microM) and inactivated by sulfite. Cyanide (1 mM) inhibited SoxF activity at pH 6.0 by 25% and at pH 8.0 by 92%. Redox titrations in the infrared spectral range from 1800 to 1200 cm(-1) and in the visible spectral range from 400 to 700 nm both yielded a midpoint potential for SoxF of -555 +/- 10 mV versus Ag/AgCl at pH 7.5 and -440 +/- 20 mV versus Ag/AgCl at pH 6.0 (-232 mV versus SHE') and a transfer of 1.9 electrons. Electrochemically induced FTIR difference spectra of SoxF as compared to those of free flavin in solution suggested a strong cofactor interaction with the apoprotein. Furthermore, an activation/variation of SoxF during the redox cycles is observed. This is the first report of a monomeric flavoprotein with sulfide dehydrogenase activity.

An exported rhodanese-like protein is induced during growth of Acidithiobacillus ferrooxidans in metal sulfides and different sulfur compounds

By proteomic analysis we found a 21-kDa protein (P21) from Acidithiobacillus ferrooxidans ATCC 19859 whose synthesis was greatly increased by growth of the bacteria in pyrite, thiosulfate, elemental sulfur, CuS, and ZnS and was almost completely repressed by growth in ferrous iron. After we determined the N-terminal amino acid sequence of P21, we used the available preliminary genomic sequence of A. ferrooxidans ATCC 23270 to isolate the DNA region containing the p21 gene. The nucleotide sequence of this DNA fragment contained a putative open reading frame (ORF) coding for a 23-kDa protein. This difference in size was due to the presence of a putative signal peptide in the ORF coding for P21. When p21 was cloned and overexpressed in Escherichia coli, the signal peptide was removed, resulting in a mature protein with a molecular mass of 21 kDa and a calculated isoelectric point of 9.18. P21 exhibited 27% identity and 42% similarity to the Deinococcus radiodurans thiosulfate-sulfur transferase (rhodanese; EC 2.8.1.1) and similar values in relation to other rhodaneses, conserving structural domains and an active site with a cysteine, both characteristic of this family of proteins. However, the purified recombinant P21 protein did not show rhodanese activity. Unlike cytoplasmic rhodaneses, P21 was located in the periphery of A. ferrooxidans cells, as determined by immunocytochemical analysis, and was regulated depending on the oxidizable substrate. The genomic context around gene p21 contained other ORFs corresponding to proteins such as thioredoxins and sulfate-thiosulfate binding proteins, clearly suggesting the involvement of P21 in inorganic sulfur metabolism in A. ferrooxidans.

Identification of a thiosulfate utilization gene cluster from the green phototrophic bacterium Chlorobium limicola

Chlorobium is an autotrophic, green phototrophic bacterium which uses reduced sulfur compounds to fix carbon dioxide in the light. The pathways for the oxidation of sulfide, sulfur, and thiosulfate have not been characterized with certainty for any species of bacteria. However, soluble cytochrome c-551 and flavocytochrome c (FCSD) have previously been implicated in the oxidation of thiosulfate and sulfide on the basis of enzyme assays in Chlorobium. We have now made a number of observations relating to the oxidation of reduced sulfur compounds. (1) Western analysis shows that soluble cytochrome c-551 in Chlorobium limicola is regulated by thiosulfate, consistent with a role in the utilization of thiosulfate. (2) A membrane-bound flavocytochrome c-sulfide dehydrogenase (which is normally a soluble protein in other species) is constitutive and not regulated by sulfide as expected for an obligately autotrophic species dependent upon sulfide. (3) We have cloned the cytochrome c-551 gene from C. limicola and have found seven other genes, which are also presumably involved in sulfur metabolism and located near that for cytochrome c-551 (SoxA). These include genes for a flavocytochrome c flavoprotein homologue (SoxF2), a nucleotidase homologue (SoxB), four small proteins (including SoxX, SoxY, and SoxZ), and a thiol-disulfide interchange protein homologue (SoxW). (4) We have established that the constitutively expressed FCSD genes (soxEF1) are located elsewhere in the genome. (5) Through a database search, we have found that the eight thiosulfate utilization genes are clustered in the same order in the Chlorobium tepidum genome (www.tigr.org). Similar thiosulfate utilization gene clusters occur in at least six other bacterial species but may additionally include genes for rhodanese and sulfite dehydrogenase.

The shxVW locus is essential for oxidation of inorganic sulfur and molecular hydrogen by Paracoccus pantotrophus GB17: a novel function for lithotrophy

The shxVW genes of Paracoccus pantotrophus were identified to be essential for lithotrophic oxidation of sulfur and hydrogen. shxV predicts a membrane protein which is 42% identical to CcdA of P. pantotrophus essential for cytochrome c biogenesis. shxW predicts a periplasmic thioredoxin. Disruption of shxV by an Omega-kanamycin interposon disabled the resulting mutant GB(Omega)V to grow with thiosulfate or molecular hydrogen and to express ShxW while cytochrome c formation was not affected. Mixotrophic growth with succinate and thiosulfate of strain GB(Omega)V revealed 2% of the thiosulfate-dependent oxygen uptake rate as compared to the wild-type while antigens of proteins essential for sulfur oxidation were present in both strains. Mixotrophic growth of strain GB(Omega)V with succinate and molecular hydrogen revealed neither hydrogenase activity nor antigens. Complementation analysis with plasmid pBHP6 carrying the shxVW genes revealed the wild-type phenotype of strain GB(Omega)V(pBHP6).

Novel genes of the sox gene cluster, mutagenesis of the flavoprotein SoxF, and evidence for a general sulfur-oxidizing system in Paracoccus pantotrophus GB17

The novel genes soxFGH were identified, completing the sox gene cluster of Paracoccus pantotrophus coding for enzymes involved in lithotrophic sulfur oxidation. The periplasmic SoxF, SoxG, and SoxH proteins were induced by thiosulfate and purified to homogeneity from the soluble fraction. soxF coded for a protein of 420 amino acids with a signal peptide containing a twin-arginine motif. SoxF was 37% identical to the flavoprotein FccB of flavocytochrome c sulfide dehydrogenase of Allochromatium vinosum. The mature SoxF (42,832 Da) contained 0.74 mol of flavin adenine dinucleotide per mol. soxG coded for a novel protein of 303 amino acids with a signal peptide containing a twin-arginine motif. The mature SoxG (29,657 Da) contained two zinc binding motifs and 0.90 atom of zinc per subunit of the homodimer. soxH coded for a periplasmic protein of 317 amino acids with a double-arginine signal peptide. The mature SoxH (32,317 Da) contained two metal binding motifs and 0.29 atom of zinc and 0.20 atom of copper per subunit of the homodimer. SoxXA, SoxYZ, SoxB, and SoxCD (C. G. Friedrich, A. Quentmeier, F. Bardischewsky, D. Rother, R. Kraft, S. Kostka, and H. Prinz, J. Bacteriol. 182:4476-4487, 2000) reconstitute a system able to perform thiosulfate-, sulfite-, sulfur-, and hydrogen sulfide-dependent cytochrome c reduction, and this system is the first described for oxidizing different inorganic sulfur compounds. SoxF slightly inhibited the rate of hydrogen sulfide oxidation but not the rate of sulfite or thiosulfate oxidation. From use of a homogenote mutant with an in-frame deletion in soxF and complementation analysis, it was evident that the soxFGH gene products were not required for lithotrophic growth with thiosulfate.

Identification of ccdA in Paracoccus pantotrophus GB17: disruption of ccdA causes complete deficiency in c-type cytochromes

A transposon Tn5-mob insertional mutant of Paracoccus pantotrophus GB17, strain TP43, was unable to oxidize thiosulfate aerobically or to reduce nitrite anaerobically, and the cellular yields were generally decreased by 11 to 20%. Strain TP43 was unable to form functional c-type cytochromes, as determined by difference spectroscopy and heme staining. However, formation of apocytochromes and their transport to the periplasm were not affected, as seen with SoxD, a c-type cytochrome associated with the periplasmic sulfite dehydrogenase homologue. The Tn5-mob-containing DNA region of strain TP43 was cloned into pSUP205 to produce pE18TP43. With the aid of pE18TP43 the corresponding wild-type gene region of 15 kb was isolated from a heterogenote recombinant to produce pEF15. Sequence analysis of 2.8 kb of the relevant region uncovered three open reading frames, designated ORFA, ccdA, and ORFB, with the latter being oriented divergently. ORFA and ccdA were constitutively cotranscribed as determined by primer extension analysis. In strain TP43 Tn5-mob was inserted into ccdA. The deduced ORFA product showed no similarity to any protein in databases. However, the ccdA gene product exhibited similarities to proteins assigned to different functions in bacteria, such as cytochrome c biogenesis. For these proteins at least six transmembrane helices are predicted with the potential to form a channel with two conserved cysteines. This structural identity suggests that these proteins transfer reducing equivalents from the cytoplasm to the periplasm and that the cysteines bring about this transfer to enable the various specific functions via specific redox mediators such as thioredoxins. CcdA of P. pantotrophus is 42% identical to a protein predicted by ORF2, and its location within the sox gene cluster coding for lithotrophic sulfur oxidation suggested a different function.

Novel genes coding for lithotrophic sulfur oxidation of Paracoccus pantotrophus GB17

The gene region coding for lithotrophic sulfur oxidation of Paracoccus pantotrophus GB17 is located on a 13-kb insert of plasmid pEG12. Upstream of the previously described six open reading frames (ORFs) soxABCDEF with a partial sequence of soxA and soxF (C. Wodara, F. Bardischewsky, and C. G. Friedrich, J. Bacteriol. 179:5014-5023, 1997), 4,350 bp were sequenced. The sequence completed soxA, and uncovered six new ORFs upstream of soxA, designated ORF1, ORF2, and ORF3, and soxXYZ. ORF1 could encode a 275-amino-acid polypeptide of 29,332 Da with a 61 to 63% similarity to LysR transcriptional regulators. ORF2 could encode a 245-amino-acid polypeptide of 26,022 Da with the potential to form six transmembrane helices and with a 48 to 51% similarity to proteins involved in redox transport in cytochrome c biogenesis. ORF3 could encode a periplasmic polypeptide of 186 amino acids of 20,638 Da with a similarity to thioredoxin-like proteins and with a putative signal peptide of 21 amino acids. Purified SoxXA, SoxYZ, and SoxB are essential for thiosulfate or sulfite-dependent cytochrome c reduction in vitro. N-terminal and internal amino acid sequences identified SoxX, SoxY, SoxZ, and SoxA to be coded by the respective genes. The molecular masses of the mature proteins determined by electrospray ionization spectroscopy (SoxX, 14,834 Da; SoxY, 11,094 Da; SoxZ, 11,717 Da; and SoxA, 30,452 Da) were identical or close to those deduced from the nucleotide sequence with differences for the covalent heme moieties. SoxXA represents a novel type of periplasmic c-type cytochromes, with SoxX as a monoheme and SoxA as a hybrid diheme cytochrome c. SoxYZ is an as-yet-unprecedented soluble protein. SoxY has a putative signal peptide with a twin arginine motif and possibly cotransports SoxZ to the periplasm. SoxYZ neither contains a metal nor a complex redox center, as proposed for proteins likely to be transported via the Tat system.

Molecular genetics of the genus Paracoccus: metabolically versatile bacteria with bioenergetic flexibility

Paracoccus denitrificans and its near relative Paracoccus versutus (formerly known as Thiobacilllus versutus) have been attracting increasing attention because the aerobic respiratory system of P. denitrificans has long been regarded as a model for that of the mitochondrion, with which there are many components (e.g., cytochrome aa3 oxidase) in common. Members of the genus exhibit a great range of metabolic flexibility, particularly with respect to processes involving respiration. Prominent examples of flexibility are the use in denitrification of nitrate, nitrite, nitrous oxide, and nitric oxide as alternative electron acceptors to oxygen and the ability to use C1 compounds (e.g., methanol and methylamine) as electron donors to the respiratory chains. The proteins required for these respiratory processes are not constitutive, and the underlying complex regulatory systems that regulate their expression are beginning to be unraveled. There has been uncertainty about whether transcription in a member of the alpha-3 Proteobacteria such as P. denitrificans involves a conventional sigma70-type RNA polymerase, especially since canonical -35 and -10 DNA binding sites have not been readily identified. In this review, we argue that many genes, in particular those encoding constitutive proteins, may be under the control of a sigma70 RNA polymerase very closely related to that of Rhodobacter capsulatus. While the main focus is on the structure and regulation of genes coding for products involved in respiratory processes in Paracoccus, the current state of knowledge of the components of such respiratory pathways, and their biogenesis, is also reviewed.

Physiology and genetics of sulfur-oxidizing bacteria

Reduced inorganic sulfur compounds are oxidized by members of the domains Archaea and Bacteria. These compounds are used as electron donors for anaerobic phototrophic and aerobic chemotrophic growth, and are mostly oxidized to sulfate. Different enzymes mediate the conversion of various reduced sulfur compounds. Their physiological function in sulfur oxidation is considered (i) mostly from the biochemical characterization of the enzymatic reaction, (ii) rarely from the regulation of their formation, and (iii) only in a few cases from the mutational gene inactivation and characterization of the resulting mutant phenotype. In this review the sulfur-metabolizing reactions of selected phototrophic and of chemotrophic prokaryotes are discussed. These comprise an archaeon, a cyanobacterium, green sulfur bacteria, and selected phototrophic and chemotrophic proteobacteria. The genetic systems are summarized which are presently available for these organisms, and which can be used to study the molecular basis of their dissimilatory sulfur metabolism. Two groups of thiobacteria can be distinguished: those able to grow with tetrathionate and other reduced sulfur compounds, and those unable to do so. This distinction can be made irrespective of their phototrophic or chemotrophic metabolism, neutrophilic or acidophilic nature, and may indicate a mechanism different from that of thiosulfate oxidation. However, the core enzyme for tetrathionate oxidation has not been identified so far. Several phototrophic bacteria utilize hydrogen sulfide, which is considered to be oxidized by flavocytochrome c owing to its in vitro activity. However, the function of flavocytochrome c in vivo may be different, because it is missing in other hydrogen sulfide-oxidizing bacteria, but is present in most thiosulfate-oxidizing bacteria. A possible function of flavocytochrome c is discussed based on biophysical studies, and the identification of a flavocytochrome in the operon encoding enzymes involved in thiosulfate oxidation of Paracoccus denitrificans. Adenosine-5'-phosphosulfate reductase thought to function in the 'reverse' direction in different phototrophic and chemotrophic sulfur-oxidizing bacteria was analysed in Chromatium vinosum. Inactivation of the corresponding gene does not affect the sulfite-oxidizing ability of the mutant. This result questions the concept of its 'reverse' function, generally accepted for over three decades.

Cloning and characterization of sulfite dehydrogenase, two c-type cytochromes, and a flavoprotein of Paracoccus denitrificans GB17: essential role of sulfite dehydrogenase in lithotrophic sulfur oxidation

A 13-kb genomic region of Paracoccus dentrificans GB17 is involved in lithotrophic thiosulfate oxidation. Adjacent to the previously reported soxB gene (C. Wodara, S. Kostka, M. Egert, D. P. Kelly, and C. G. Friedrich, J. Bacteriol. 176:6188-6191, 1994), 3.7 kb were sequenced. Sequence analysis revealed four additional open reading frames, soxCDEF. soxC coded for a 430-amino-acid polypeptide with an Mr of 47,339 that included a putative signal peptide of 40 amino acids (Mr of 3,599) with a RR motif present in periplasmic proteins with complex redox centers. The mature soxC gene product exhibited high amino acid sequence similarity to the eukaryotic molybdoenzyme sulfite oxidase and to nitrate reductase. We constructed a mutant, GBsoxC delta, carrying an in-frame deletion in soxC which covered a region possibly coding for the molybdenum cofactor binding domain. GBsoxC delta was unable to grow lithoautotrophically with thiosulfate but grew well with nitrate as a nitrogen source or as an electron acceptor. Whole cells and cell extracts of mutant GBsoxC delta contained 10% of the thiosulfate-oxidizing activity of the wild type. Only a marginal rate of sulfite-dependent cytochrome c reduction was observed from cell extracts of mutant GBsoxC delta. These results demonstrated that sulfite dehydrogenase was essential for growth with thiosulfate of P. dentrificans GB17. soxD coded for a periplasmic diheme c-type cytochrome of 384 amino acids (Mr of 39,983) containing a putative signal peptide with an Mr of 2,363. soxE coded for a periplasmic monoheme c-type cytochrome of 236 amino acids (Mr of 25,926) containing a putative signal peptide with an Mr of 1,833. SoxD and SoxE were highly identical to c-type cytochromes of P. denitrificans and other organisms. soxF revealed an incomplete open reading frame coding for a peptide of 247 amino acids with a putative signal peptide (Mr of 2,629). The deduced amino acid sequence of soxF was 47% identical and 70% similar to the sequence of the flavoprotein of flavocytochrome c of Chromatium vinosum, suggesting the involvement of the flavoprotein in thiosulfate oxidation of P. denitrificans GB17.

Transposon mutagenesis affecting thiosulfate oxidation in Bosea thiooxidans, a new chemolithoheterotrophic bacterium

Transposon insertion mutagenesis was used to isolate mutants of Bosea thiooxidans which are impaired in thiosulfate oxidation. Suicide plasmid pSUP5011 was used to introduce the transposon Tn5 into B. thiooxidans via Escherichia coli S17.1-mediated conjugation. Neomycin-resistant transconjugants occurred at a frequency of 2.2 X 10(-4) per donor. Transconjugants defective in thiosulfate oxidation were categorized into three classes on the basis of growth response, enzyme activities, and cytochrome patterns. Class I mutants were deficient in cytochrome c, and no thiosulfate oxidase activity was detected. Class II mutants retained the activities of key enzymes of thiosulfate metabolism, although at reduced levels. Mutants of this class grown on mixed-substrate agar plates deposited elemental sulfur on the colony surfaces. Class III mutants were unable to utilize thiosulfate, though they had normal levels of cytochrome c. The transposon insertions occurred at different chromosomal positions, as confirmed by Southern blotting of chromosomal DNA of mutants deficient in thiosulfate oxidation, a deficiency which resulted from single insertions of Tn5.

Identification and sequence analysis of the soxB gene essential for sulfur oxidation of Paracoccus denitrificans GB17

The coding region for lithotrophic sulfur oxidation (Sox) in Paracoccus denitrificans GB17 was identified by isolation of a transposon Tn5-mob mutant with a Sox- phenotype (strain TP19). The corresponding wild-type region was cloned previously (G. Mittenhuber, K. Sonomoto, M. Egert, and C. G. Friedrich, J. Bacteriol. 173:7340-7344, 1991). Sequence analysis of a 2.5-kb subclone that complemented strain TP19 revealed that Tn5-mob was inserted into a coding region for a 553-amino-acid polypeptide named SoxB. This polypeptide had an M(r) of 60.573, including a possible signal peptide. The function of the SoxB protein of P. denitrificans GB17 appeared to be identical to that of enzyme B of the thiosulfate-oxidizing enzyme system of Thiobacillus versutus. The amino acid compositions of the two proteins were identical, and the amino acid sequences of three internal peptides of enzyme B as determined by Edman degradation were identical to corresponding sequences of the deduced SoxB protein of P. denitrificans GB17.

Differential reduction in soluble and membrane-bound c-type cytochrome contents in a Paracoccus denitrificans mutant partially deficient in 5-aminolevulinate synthase activity

A mutant of Paracoccus denitrificans, DP104, unable to grow anaerobically with nitrate as the terminal electron acceptor or aerobically with methanol as the electron donor and staining negatively in the dimethylphenylene diamine oxidation (Nadi) test, was isolated by transposon Tn5::phoA mutagenesis. P. denitrificans DP104 grown aerobically with succinate or choline had very low levels (2 to 3% of the wild-type levels) of spectroscopically detectable soluble c-type cytochromes. In contrast, membrane cytochromes of the a, b, and c types were present at 50% of the levels found in the wild type. The apo form of cytochrome c550, at an approximately 1:1 molar ratio with the holo form, was found in the periplasm of DP104. The TnphoA element was shown to be inserted immediately upstream of the translational start of hemA, the gene coding for 5-aminolevulinate synthase, which was sequenced. Low-level expression of this gene, driven off an incidental promoter provided by TnphoA-cointegrated suicide vector DNA, is the basis of the phenotype which could be complemented by the addition of 5-aminolevulinate to growth media. Disruption of the hemA gene generated a P. denitrificans strain auxotrophic for 5-aminolevulinate, establishing that there is no hemA-independent pathway of heme synthesis in this organism. The differential deficiency in periplasmic c-type cytochromes relative to membrane cytochromes in DP104 is suggested to arise from unequal competition for the restricted supply of heme which results from the effects of the transposon insertion.

Sulfide dehydrogenase is identical with the SoxB protein of the thiosulfate-oxidizing enzyme system of Paracoccus denitrificans GB17

Thiosulfate induced cells of Paracoccus denitrificans GB17 oxidize thiosulfate and sulfide to sulfate. A mutant carrying a Tn5-mob insertion in the soxB gene is unable to oxidize thiosulfate or sulfide suggesting a linkage of both activities. To test this assumption we have separated the components of the thiosulfate-oxidizing enzyme system of the wild-type by ion exchange chromatography. The SoxB protein coeluted with a highly active sulfide dehydrogenase. Analysis by polyacrylamide gel electrophoresis revealed one major protein of M(r) 32k. Thus, the SoxB protein appeared to be identical with sulfide dehydrogenase.

Transfer and expression of degradative and antibiotic resistance plasmids in acidophilic bacteria

The genetic accessibility of selected acidophilic bacteria was investigated to evaluate their applicability to degrading pollutants in acidic environments. The IncP1 antibiotic resistance plasmids RP4 and pVK101 and the phenol degradation-encoding plasmid pPGH11 were transferred from neutrophilic bacteria into the extreme acidophilic eubacterium Acidiphilium cryptum at frequencies of 1.8 x 10(-2) to 9.8 x 10(-4) transconjugants per recipient cell. The IncQ antibiotic resistance plasmid pSUP106 was mobilizable to A. cryptum by triparental matings at a frequency of 10(-5) transconjugants per recipient cell. In the transconjugants, antibiotic resistances and the ability to degrade phenol were expressed. A. cryptum AC6 (pPGH11) grew with 2.5 mM phenol at a doubling time of 12 h and a yield of 0.52 g (dry cell weight) per g of phenol. A. cryptum harbored five native plasmids of 255 to 6.3 kb in size. Plasmids RP4 and pVK101 were transferred from Escherichia coli into Acidobacterium capsulatum at frequencies of 10(-3) and 2.3 x 10(-4) and to the facultative autotroph Thiobacillus acidophilus at frequencies of 1.1 x 10(-5) and 2.9 x 10(-6) transconjugants per recipient cell, respectively. Plasmid pPGH11 could not be transferred into the latter strains. T. acidophilus wild type contained six so far cryptic plasmids of 220 to 5 kb.

The purification of a cd1-type nitrite reductase from, and the absence of a copper-type nitrite reductase from, the aerobic denitrifier Thiosphaera pantotropha; the role of pseudoazurin as an electron donor

Thiosphaera pantotropha has been reported to contain a copper-type nitrite reductase on the basis that the copper chelator diethyldithiocarbamate inhibited the overall process of denitrification. It is now shown that nitrous oxide reduction is 100% inhibited by 10 mM diethyldithiocarbamate or 100 microM azide. We also found that both these inhibitors partially inhibited nitrite reduction in this organism. We purified the nitrite reductase of T. pantotropha and found that it was of the cytochrome cd1 type, contrary to the published report of it being a copper-type nitrite reductase. This is of importance since T. pantotropha is capable of aerobic nitrite reduction. The only detectable nitrite reductase in anaerobically or aerobically grown cells is the cd1 type. We also purified a small copper-containing protein, pseudoazurin. Pseudoazurin was found to be capable of donating electrons to the cd1-type nitrite reductase in vitro, and its copper centre was chelated by diethyldithiocarbamate. Since nitrite reduction is partially inhibited by diethyldithiocarbamate, it is thought that pseudoazurin is an electron donor to nitrite reductase in vivo.

Identification of the DNA region responsible for sulfur-oxidizing ability of Thiosphaera pantotropha

For the identification of the DNA region responsible for the sulfur-oxidizing ability (Sox) of Thiosphaera pantotropha, we used previously isolated Tn5-mob insertional Sox- mutants. For seven mutants, the Tn5-mob insertion was localized on the chromosome rather than on the megaplasmids pHG41 or pHG42 by using the Tn5-mob-harboring vehicle pSUP5011 as probe. The specific insertion of Tn5-mob into a sox gene was determined for one Sox- mutant, strain TP19. An 18-kb EcoRI fragment was cloned in Escherichia coli by using the mobilizable plasmid pSUP202 as vector and the kanamycin resistance gene of Tn5 as marker. Conjugal transfer of the resulting hybrid plasmid, pKS3-13, to the wild type resulted in two phenotypically different groups of recombinants. Ninety-five percent of the recombinants were Sox+, kanamycin resistant, and tetracycline resistant; 5% were homogenote recombinants exhibiting the Sox-, kanamycin-resistant, tetracycline-sensitive phenotype, and these indicated the specific insertion. To isolate the respective wild-type sox gene, total DNA from a heterogenote recombinant was partially restricted with EcoRI, religated, and transformed in E. coli. Transformants carrying a pSUP202-derived hybrid plasmid with the intact sox gene were identified by screening for a tetracycline-resistant, kanamycin-sensitive, and chloramphenicol-sensitive phenotype and by complementation of the Sox- mutant TP19. A plasmid of this type, pEG12, contained an insert of 13 kb which gave a positive signal in Southern hybridization with the homologous probe of pKS3-13. pEG12 was used to determine the DNA homology of the sulfur-oxidizing enzyme systems of other thiobacteria. Strong hybridization signals were obtained with total DNA of the neutrophilic sulfur-oxidizing bacteria Paracoccus denitrificans, Thiobacillus versutus, and Rhodobacter capsulatus. No hybridization signal was obtained with DNA of other neutrophilic or acidophilic thiobacteria examined.

Combined heterotrophic nitrification and aerobic denitrification in Thiosphaera pantotropha and other bacteria

Reports of the simultaneous use of oxygen and denitrification by different species of bacteria have become more common over the past few years. Research with some strains (e.g. Thiosphaera pantotropha) has indicated that there might be a link between this 'aerobic denitrification' and a form of nitrification which requires rather than generates energy and is therefore known as heterotrophic nitrification. This paper reviews recent research into heterotrophic nitrification and aerobic denitrification, and presents a preliminary model which, if verified, will provide at least a partial explanation for the simultaneous occurrence of nitrification and denitrification in some bacteria.

Molecular and cellular regulation of autotrophic carbon dioxide fixation in microorganisms

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Purification and properties of a protein linked to the soluble hydrogenase of hydrogen-oxidizing bacteria

In Alcaligenes eutrophus, the formation of the hydrogenases and of five new peptides is subject to the hydrogenase control system. Of these, the B peptide was purified to homogeneity. This protein (Mr, 37,500) was composed of two identical subunits (Mr, 18,800). Antibodies against the B protein were used for its quantification by rocket immunoelectrophoresis. About 4% of the total protein consisted of the B protein; its molar ratio to the NAD-linked hydrogenase was about 4:1. The B protein appeared to be associated with the NAD-linked hydrogenase, as shown by gel filtration analysis with Sephadex G-200. The B protein was not detected in cells that had not expressed the hydrogenase proteins or that lacked the genetic information of the hydrogen-oxidizing character; it was also not detected in Tn5 insertional mutants that were unable to form soluble hydrogenase antigens. Immunochemical analysis of other species and genera than A. eutrophus revealed that only strains able to form a NAD-linked hydrogenase also formed B-protein antigens. The B protein is not required for the catalytic activity of soluble hydrogenase in vitro; its function is at present unknown.