Novel Genes Coding for Lithotrophic Sulfur Oxidation of
            <i>Paracoccus pantotrophus</i>
            GB17

Friedrich, Cornelius G.; Quentmeier, Armin; Bardischewsky, Frank; Röther, Dagmar; Kraft, Regine; Kostka, Susanne; Prinz, Heino

doi:10.1128/jb.182.17.4677-4687.2000

Cited by 145 publications

(194 citation statements)

References 54 publications

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“…The soxB gene from fosmid_ soxB1 was separated from other sox genes, as has been observed in T. crunogena . The soxB from fosmid_soxB2 was linked with other sox genes to form a soxXYZAB cluster on the Comparative metagenomics of two chimneys W Xie et al chromosome, but the single sox operon that has been described in facultative autotrophic sulfur-oxidizers, such as Paracoccus versutus and Rhodopseudomonas palustris (Schutz et al, 1999;Friedrich et al, 2000; Figure 5) was not found. Obligate autotrophic sulfur-oxidizers appear to not have the complete set of the sox genes organized in a single operon as observed in facultative autotrophs, possibly because the sox genes are constitutively expressed and, therefore, the sox gene organization into a single operon may not be strongly evolutionarily selected .…”

Section: Sulfur Oxidationmentioning

confidence: 99%

Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries

Xie

Wang

Guo³

et al. 2010

The ISME Journal

158

131

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Deep-sea hydrothermal vent chimneys harbor a high diversity of largely unknown microorganisms. Although the phylogenetic diversity of these microorganisms has been described previously, the adaptation and metabolic potential of the microbial communities is only beginning to be revealed. A pyrosequencing approach was used to directly obtain sequences from a fosmid library constructed from a black smoker chimney 4143-1 in the Mothra hydrothermal vent field at the Juan de Fuca Ridge. A total of 308 034 reads with an average sequence length of 227 bp were generated. Comparative genomic analyses of metagenomes from a variety of environments by two-way clustering of samples and functional gene categories demonstrated that the 4143-1 metagenome clustered most closely with that from a carbonate chimney from Lost City. Both are highly enriched in genes for mismatch repair and homologous recombination, suggesting that the microbial communities have evolved extensive DNA repair systems to cope with the extreme conditions that have potential deleterious effects on the genomes. As previously reported for the Lost City microbiome, the metagenome of chimney 4143-1 exhibited a high proportion of transposases, implying that horizontal gene transfer may be a common occurrence in the deep-sea vent chimney biosphere. In addition, genes for chemotaxis and flagellar assembly were highly enriched in the chimney metagenomes, reflecting the adaptation of the organisms to the highly dynamic conditions present within the chimney walls. Reconstruction of the metabolic pathways revealed that the microbial community in the wall of chimney 4143-1 was mainly fueled by sulfur oxidation, putatively coupled to nitrate reduction to perform inorganic carbon fixation through the Calvin-Benson-Bassham cycle. On the basis of the genomic organization of the key genes of the carbon fixation and sulfur oxidation pathways contained in the large genomic fragments, both obligate and facultative autotrophs appear to be present and contribute to biomass production.

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Section: Sulfur Oxidationmentioning

confidence: 99%

Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries

Xie

Wang

Guo³

et al. 2010

The ISME Journal

158

131

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“…In P. pantotrophus the thioredoxin-encoding soxW gene (formerly shxW) is expressed in the presence of thiosulfate ), as are the structural genes soxXYZABCD and subsequent genes soxEFGH of unknown function (Friedrich et al, 2000;Rother et al, 2001). In the mutant strain P. pantotrophus GBVV the soxV gene (formerly shxV) is disrupted by the V-kanamycin interposon.…”

Section: Introductionmentioning

confidence: 99%

SoxRS-mediated regulation of chemotrophic sulfur oxidation in Paracoccus pantotrophus

et al. 2005

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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 GBVS carrying a disruption of soxS by the V-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 His 6 -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.

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“…Genetic studies with both chemo-and photolithotrophic sulfur-oxidizing a-proteobacteria like Paracoccus pantotrophus, Pseudaminobacter salicylatoxidans KCT001 and Rhodovulum sulfidophilum have recently led to the identification of a cluster of sulfur oxidation (sox) genes, viz. soxVW and soxXYZABCDEFGH (Friedrich et al, 2000;Mukhopadhyaya et al, 2000;Rother et al, 2001;AppiaAyme & Berks, 2002). A consensus mechanism allegedly governing the complete oxidation of thiosulfate, sulfite, sulfide and elemental sulfur has been proposed with a-proteobacteria as model systems involving a sulfuroxidizing multi-enzyme complex comprising the thiosulfate-induced periplasmic proteins SoxXA, SoxYZ, SoxB and SoxCD (Friedrich, 1998;Appia-Ayme et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

The dimeric repressor SoxR binds cooperatively to the promoter(s) regulating expression of the sulfur oxidation (sox) operon of Pseudaminobacter salicylatoxidans KCT001

et al. 2007

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Sulfur oxidation in Pseudaminobacter salicylatoxidans KCT001 is rendered by the combined action of several enzymes encoded by a thiosulfate-inducible sox operon. In this study it has been conclusively demonstrated by insertional mutagenesis that the regulatory gene of this operon is soxR, which encodes a DNA-binding protein belonging to the ArsR-SmtB family. SoxR was found to bind to two promoter-operator segments within the sox cluster, of which the one (wx) located between soxW and soxX controls the expression of sulfur-oxidation genes soxX through soxD while the other, a bi-directional element (sv) located between soxS and soxV, controls the expression of soxVW in one direction and the putative regulatory cluster soxSRT in the other. In the case of the wx promoter the repressor was found to bind in a cooperative manner to two distinct binding sites having different affinities, while in the case of the sv promoter binding occurred at a symmetric dimeric site and involved a higher degree of cooperativity. The high degree of cooperativity observed in the binding of SoxR to its target sites seemed to be due to the propensity of SoxR monomers to form dimers. The apparent dissociation constants of the SoxR-operator complexes were in the nanomolar range, indicating relatively strong interactions. It was demonstrated using a reporter system in Escherichia coli that this high-affinity binding of SoxR led to efficient repression in trans. Thus the role of SoxR as a repressor of the sox operon has not only been conclusively established but it has also been shown that this repression is brought about through cooperative interactions of SoxR with dimeric binding sites that occlude the operon promoters.

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Novel Genes Coding for Lithotrophic Sulfur Oxidation of Paracoccus pantotrophus GB17

Cited by 145 publications

References 54 publications

Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries

Comparative metagenomics of microbial communities inhabiting deep-sea hydrothermal vent chimneys with contrasting chemistries

SoxRS-mediated regulation of chemotrophic sulfur oxidation in Paracoccus pantotrophus

The dimeric repressor SoxR binds cooperatively to the promoter(s) regulating expression of the sulfur oxidation (sox) operon of Pseudaminobacter salicylatoxidans KCT001

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