Cloning and sequencing of a [NiFe] hydrogenase operon from Desulfovibrio vulgaris Miyazaki F

Deckers, Harm M.; Wilson, Frankie R.; Voordouw, Gerrit

doi:10.1099/00221287-136-10-2021

Cited by 47 publications

(31 citation statements)

References 22 publications

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“…Three types of hydrogenases have been found from the genus Desulfovibrio in sulfate-reducing bacteria (Prickril et al, 1987), and they are classified as Fe, NiFe and NiFeSe hydrogenases. The hydrogenase in this study is grouped into the NiFe hydrogenases and, from the amino-acid sequence, it is considered to contain two Fe4S4 clusters, one Fe3S4 cluster and one Ni atom as prosthetic groups (Deckers, Wilson & Voordouw, 1990;Furuichi, Ozaki, Niki & Akutsu, 1990). The presence and the content of Ni and Fe atoms in the hydrogenase from Miyazaki was confirmed by the K-edge jump of extended X-ray absorption fine-structure spectroscopy (EXAFS) data (Yasuoka et al, 1993).…”

Section: Introductionmentioning

confidence: 92%

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Location of active sites of NiFe hydrogenase determined by the combination of multiple isomorphous replacement and multiwavelength anomalous-diffraction methods

Higuchi¹,

Okamoto²,

Fujimoto³

et al. 1994

Acta Cryst D

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The active centers of NiFe hydrogenase from Desulfovibrio vulgaris Miyazaki F have been located in the electron-density map calculated at 4 A resolution. The electron-density map based on five heavy-atom derivatives showed four strong peaks which were clearly distinguished from the protein region. These strong densities have been successfully assigned to three iron-sulfur clusters and one Ni atom by a difference Fourier technique with coefficients of the best phases from the multiple isomorphous replacement (MIR) method and structure factors obtained at five wavelengths (1.040, 1.487, 1.730, 1.743 and 1.750 A) with the use of a synchrotron radiation source. Four active centers are approximately lined up at a distance of ca 13 .~, which seems reasonable if they are connected with the electron-transfer chain.

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Section: Introductionmentioning

confidence: 92%

“…Its amino-acid sequence was recently determined from the gene sequence (Deckers, Wilson & Voordouw, 1990). Three types of hydrogenases have been found from the genus Desulfovibrio in sulfate-reducing bacteria (Prickril et al, 1987), and they are classified as Fe, NiFe and NiFeSe hydrogenases.…”

Section: Introductionmentioning

confidence: 99%

Location of active sites of NiFe hydrogenase determined by the combination of multiple isomorphous replacement and multiwavelength anomalous-diffraction methods

Higuchi¹,

Okamoto²,

Fujimoto³

et al. 1994

Acta Cryst D

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“…In the present study, the dot blot and DNA hybridization results showed homology of the SRB DNA with gene probes of smtAB encoding bacterial metallothionein (20), cadAC encoding P-type ATPase (26), and cadD (9) encoding metal-binding protein. DNA hybridization has been used to detect the hydrogenase and cytochrome genes in SRB (10,51). The technique has also been widely used for the detection of homologous metal resistance determinants in many other species of bacteria (20,26,56).…”

Section: Discussionmentioning

confidence: 99%

Cadmium Accumulation and DNA Homology with Metal Resistance Genes in Sulfate-Reducing Bacteria

Naz

Young

Ahmed

et al. 2005

Appl Environ Microbiol

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Cadmium resistance (0.1 to 1.0 mM) was studied in four pure and one mixed culture of sulfate-reducing bacteria (SRB). The growth of the bacteria was monitored with respect to carbon source (lactate) oxidation and sulfate reduction in the presence of various concentrations of cadmium chloride. Two strains Desulfovibrio desulfuricans DSM 1926 and Desulfococcus multivorans DSM 2059 showed the highest resistance to cadmium (0.5 mM). Transmission electron microscopy of the two strains showed intracellular and periplasmic accumulation of cadmium. Dot blot DNA hybridization using the probes for the smtAB, cadAC, and cadD genes indicated the presence of similar genetic determinants of heavy metal resistance in the SRB tested. DNA sequencing of the amplified DNA showed strong nucleotide homology in all the SRB strains with the known smtAB genes encoding synechococcal metallothioneins. Protein homology with the known heavy metal-translocating ATPases was also detected in the cloned amplified DNA of Desulfomicrobium norvegicum I1 and Desulfovibrio desulfuricans DSM 1926, suggesting the presence of multiple genetic mechanisms of metal resistance in the two strains.Many genetic systems are known in bacteria for maintaining intracellular homeostasis of essential metal ions and for acquiring resistance against toxic metals (44). Two well-studied genetic mechanisms of metal resistance in bacteria include heavy metal efflux systems (30) and the presence of metal binding proteins (32,39).Many operons of the efflux system are known, for example, the cadA operon (26), in which a P-type ATPase is involved in metal ion transport across the cell membranes (3). The cadA operon is composed of two genes designated cadA and cadC (44). cadA acts as a P-type ATPase, while cadC acts as a regulatory gene of cadA. The cadA operon has been reported to provide cadmium resistance in Bacillus subtilis (48), Staphylococcus aureus (31), Stenotrophomonas maltophilia (1), Pseudomonas putida (28), Listeria monocytogenes (26), and Helicobacter pylori (17). The cadA homolog zntA has been reported in Escherichia coli (5, 38), which acts as a Zn, Cd, and Pb translocating P-type ATPase pump. Another cadA homologue, ziaA, has been shown to confer Zn and Cd tolerance in Synechococcus sp. strain PCC 6803 (47).A plasmid-mediated metal resistance mechanism in Staphylococcus aureus is governed by the cadB operon, with two genes designated cadB and cadX (35). It has been suggested that cadB provides protection by enabling cells to bind cadmium in their cell membranes (35). Chromosomal DNA mediated cadmium resistance gene cadD in Staphylococcus aureus (9) has shown sequence similarity with the cadB-like gene from Staphylococcus lugdunensis (7).Another mechanism of metal detoxification and homeostasis that involves metal-binding proteins is mediated by metallothionein-encoding genes (39). Metallothioneins are small, cysteine-rich proteins (15), synthesized under heavy metal stress conditions that have been found in both prokaryotes (32, 39) and eukaryotes (33). The ...

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“…HydA and HydB of W. succinogenes are homologous to the corresponding subunits of ten other membrane Ni-hydrogenases [36,[42][43][44][45][46][47][48][49] (Table 3). There is 35-45% sequence identity among the HydA and 26-34% among the HydB subunits.…”

Section: H Y D Cmentioning

confidence: 99%

The quinone‐reactive Ni/Fe‐hydrogenase of Wolinella succinogenes

Dross

Geisler

Lenger

et al. 1992

European Journal of Biochemistry

129

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The hydrogenase (Hyd) isolated from the cytoplasmic membrane of Wolinellu succinogenes consists of three polypeptides (HydA, HydB and HydC) and contains cytochrome h (6.4 pmol/g protein), which was reduced upon the addition of H2. The enzyme catalyzed the reduction of 2,3-dimethyl-1, 4-naphthoquinone with H2, in contrast to an earlier preparation which was made up of HydA and HydB only and did not contain cytochrome b (Unden, G., Bocher, R., Knecht, J. & Kroger, A. (1982) FEBS Lett. 145, 230-234). This suggests that HydC is a cytochrome b which serves as a mediator in the electron transfer from H2 to the quinone.The hydrogenase genes were cloned, sequenced and identified by sequence comparison with the N-termini of the three subunits. The three genes were arranged in the order hydA, hydB, hydC, with the transcription start site in front of hydA, and were present only once on the genome. Separated by an intergene region of 69 nucleotides, hydC was followed by at least two more open reading frames of unknown function. The amino acid sequences derived from hydA, hydB and hydC were similar to those of the membrane Ni-hydrogenases of seven other bacteria. HydA and HydB also showed similarity to the small and the large subunits of periplasmic Ni-hydrogenases. HydC was predicted to contain four hydrophobic segments which might span the bacterial membrane. Two histidine residues located in hydrophobic segments are conserved in the corresponding sequences of the other membrane hydrogenases and might ligate the haem B.

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Cloning and sequencing of a [NiFe] hydrogenase operon from Desulfovibrio vulgaris Miyazaki F

Cited by 47 publications

References 22 publications

Location of active sites of NiFe hydrogenase determined by the combination of multiple isomorphous replacement and multiwavelength anomalous-diffraction methods

Location of active sites of NiFe hydrogenase determined by the combination of multiple isomorphous replacement and multiwavelength anomalous-diffraction methods

Cadmium Accumulation and DNA Homology with Metal Resistance Genes in Sulfate-Reducing Bacteria

The quinone‐reactive Ni/Fe‐hydrogenase of Wolinella succinogenes

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