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Applied and Environmental Microbiology, April 2002, p. 1932-1937, Vol. 68, No. 4
0099-2240/02/$04.00+0 DOI: 10.1128/AEM.68.4.1932-1937.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019
Received 4 October 2001/ Accepted 2 January 2002
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For years, a debate over the mechanism by which lactate is oxidized in SRB has existed. In 1981, Odom and Peck proposed the hydrogen-cycling model for growth on lactate (12). In this model, electrons from lactate are used by a cytoplasmic hydrogenase to generate hydrogen that can diffuse out across the cell membrane to be utilized by periplasmic dehydrogenases. Membrane potential is generated as protons remain in the periplasm while electrons are transferred across the cell membrane to reduce sulfate. When only hydrogen is utilized as an electron donor, it is likely oxidized in the periplasm by hydrogenases, but it may use different electron carriers in the reduction of sulfate than electrons generated during lactate oxidation.
We know that lactate dehydrogenase, pyruvate-ferredoxin oxidoreductase, phosphotransacetylase, and acetate kinase convert lactate to acetate and that ATP sulfurylase, pyrophosphatase, adenosine-5'-phosphosulfate (APS) reductase, and bisulfite reductase are responsible for linking electrons produced with sulfate reduction (13). Unfortunately, the identity of electron carriers involved in lactate and hydrogen metabolism remains elusive and has prompted a few biochemical and molecular studies in recent years in hopes of better defining this process. Voordouw et al. (18) examined the distribution of cytoplasmic and periplasmic hydrogenases for 22 Desulfovibrio species and determined that only the genes for periplasmic [NiFe] hydrogenase were present in all species surveyed. This finding challenged the hydrogen-cycling model, which requires SRB to possess a cytoplasmic hydrogenase (possibly an [NiFeSe] hydrogenase) in addition to a periplasmic hydrogenase. Discovery of the hmc operon in Desulfovibrio vulgaris Hildenborough offered a solution as to how electrons in the periplasm could reach the cytoplasmic sulfate reduction enzymes (14, 15). By using antibodies to HmcA and HmcF, expression of the hmc operon in D. vulgaris was found to be highest during growth on hydrogen (8). Deletion of the hmc operon in D. vulgaris (Hildenborough) impaired growth on hydrogen but not that on lactate or pyruvate, confirming the importance of the Hmc complex in electron transport from hydrogen in the periplasm to sulfate in the cytoplasm (4).
This study was originally intended to evaluate the applicability of random arbitrarily primed PCR (RAP-PCR) to environmental bacteria that reduce sulfate, but initial findings led us to probe further into differential expression of SRB redox proteins. We used a combination of RAP-PCR and Northern blotting to identify genes that were differentially transcribed under conditions of growth with either hydrogen or lactate as an electron donor. After the observation that bisulfite reductase was transcribed to higher levels in hydrogen-grown cells than in lactate-grown cells, differential transcription of other known redox proteins, including [NiFe] hydrogenase and HmcA, was characterized by Northern blotting.
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RNA extraction.
Total RNA was isolated as described by Shepard and Gilmore (17), with minor modifications to the procedure. Mid-log-phase cells for D. desulfuricans strain Essex 6 and late log cells for D. desulfuricans subsp. aestuarii were harvested by centrifugation for 5 min at 7,000 x g. The pellet was resuspended in 1 ml of Tri Reagent (Sigma) and transferred to sterile tubes containing 0.5 ml of 100-µm-diameter zirconia-silicon beads. Cells were broken in a Mini-Beadbeater (Biospec Products) for 1 min. The supernatant was extracted with 300 µl of chloroform and placed on ice for 15 min. After centrifugation for 10 min (12,000 x g), nucleic acids in the aqueous phase were precipitated with 750 µl of isopropyl alcohol and placed on ice for 10 min. Following centrifugation and a 75% ethanol wash, pellets were resuspended in 200 µl of diethyl pyrocarbonate (DEPC)-treated water. Contaminating genomic DNA was removed by addition of 22 µl of Multi Core Restriction Enzyme Buffer (Promega) and 5 U of RNase-free DNase (Stratagene) with incubation at 37°C for 15 min. Following this treatment, 500 µl of phenol-chloroform-isoamyl alcohol was added and centrifuged (12,000 x g, 10 min). The aqueous phase was removed, and the phenolic phase was extracted a second time with 250 µl of DEPC-treated water. After centrifugation, this second aqueous phase was mixed with the first, and RNA was precipitated with 1 ml of 100% ethanol for at least 30 min at -80°C. RNA was pelleted by centrifugation (12,000 x g, 30 min), washed with 75% ethanol, resuspended in 0.1 mM EDTA, and stored at -80°C. Integrity of RNA was determined by 0.8% agarose electrophoresis in Tris-borate-EDTA buffer, and the concentration was determined by measuring the A260/A280 ratio spectrophotometrically (16).
RAP-PCR.
RAP-PCR was performed as described by Shepard and Gilmore (17). For each reaction, 14.5 µl containing 1 µg of total RNA, diluted in DEPC-treated water when necessary, was heated to 70°C for 10 min and placed on ice. After a 1-min incubation on ice, 2 µl of reverse transcription buffer (Fisher), 40 U of RNase Block RNase inhibitor (Stratagene), a 1.25 mM concentration of each deoxynucleoside triphosphate, and a 1.25 µM concentration of arbitrary primer (Stratagene) were added. After the contents were mixed, the reaction mixture was held at 37°C for 5 min. After equilibration, 25 U of Moloney murine leukemia virus reverse transcriptase (RT) (Stratagene) was added. First-strand cDNA synthesis occurred at 37°C for 1 h, and then the reaction mixture was heated to 90°C for 5 min to inactivate the RT and placed on ice for 10 min. For second-strand synthesis, 10 µl of a 1:10 dilution of first-strand cDNA product was mixed with 39.8 µl of standard PCR mix containing Taq buffer without MgCl2 (Sigma), 3 mM MgCl2, a 50 µM concentration of each deoxynucleoside triphosphate, 10 µCi of [
-33P]dCTP, and a 1 µM concentration of the same arbitrary primer used in first-strand synthesis for a final reaction volume of 50 µl. The reaction mixture was heated to 96°C for 10 min following overlay with 50 µl of light mineral oil. After incubation at 36°C for 15 min, 1 U of Taq polymerase (Sigma) was added to each reaction mixture. The reaction continued to equilibrate for another 15 min at 36°C, followed by incubation at 72°C for 5 min. For the remaining 39 cycles of PCR, the following parameters were used: 94°C (1 min), 50°C (1 min), 72°C (2 min), and a final extension at 72°C for 10 min. The reaction mixture was stored at 4°C. Products were resolved on a 6% polyacrylamide gel (Life Technologies) prepared in Tris-borate-EDTA buffer and run at 1,500 V until the xylene cyanol dye migrated to the bottom of the gel. The gel was transferred to 3MW paper (Midwest Scientific, Valley Park, Mo.) and dried under vacuum at 70°C for 45 min. The gel was exposed to Kodak BioMax MR film for 12 h at room temperature. Putative differentially transcribed bands were excised from the gel, eluted from the filter paper with elution buffer (0.5 M ammonium acetate, 10 mM magnesium acetate, 1 mM EDTA, 0.1% sodium dodecyl sulfate), precipitated with 100% ethanol, and resuspended in 10 µl of sterile water. The cDNA was then reamplified with the PCR parameters used in second-strand synthesis and resolved on a 6% polyacrylamide gel with the original RAP-PCR product for comparison to ensure that the correct band was isolated. The candidate PCR product was ligated into pCR4-TOPO vector and transformed into chemically competent One Shot TOP10 Escherichia coli (Invitrogen). Plasmid was isolated from 2 ml of liquid cultures of candidate clones grown in Luria broth plus ampicillin (50 µg/ml) by using a miniprep plasmid isolation kit (Qiagen) according to the manufacturer's directions. DNA sequencing was carried out at the Oklahoma Medical Research Foundation Core Sequencing Facility. Typically three clones were sequenced per transformation. Candidate inserts ranged in size from 328 to 1,026 bases. GenBank sequence comparison was performed by both nucleotide and protein BLAST searches (19).
Confirmation of differential gene transcription.
RNA probes were prepared from plasmids isolated from RAP-PCR clones. Plasmids were first digested with NotI or PstI to linearize DNA prior to transcription. Linearized DNA (0.2 µg) in RNA polymerase buffer (Ambion); 4 mM (each) ATP, CTP, and GTP; and [
-32P]UTP was incubated with either T3 DNA-dependent RNA polymerase or T7 DNA-dependent RNA polymerase (depending on orientation) at 37°C for 60 min. RNase-free DNase (1 U) was added and left for an additional 30 min to remove plasmid and template DNAs. The mixture was diluted 20-fold, and unincorporated radiolabeled nucleotide was separated from the probe with a Sephadex G-50 column. At least 106 cpm of labeled RNA probe was added to each hybridization mixture. For the RNA blots, 20 µg of total RNA from both growth conditions was loaded onto a 1.5% agarose gel containing 15% formaldehyde and 1x MOPS [3-(N-morpholino)propanesulfonic acid]. RNA was electrophoresed for 2 h at 150 V with 0.5x MOPS as the running buffer. The gel was transferred overnight with a Turboblotter to Nytran SuPerCharge nylon membranes according to the directions of the manufacturer (Schleicher and Schuell). The membrane was cross-linked to RNA with UV at 125 mJ/cm2 for 1 min. The membrane was then exposed to a standard prehybridization buffer for 6 h at 65°C and then to hybridization buffer and probe for 12 h at 65°C. Washings were performed with 1x SSPE (0.18 M NaCl, 10 mM NaH2PO4, and 1 mM EDTA [pH 7.7]) with 0.1% sodium dodecyl sulfate at room temperature (three times for 5 min each) and at 65°C (three times for 30 min each). Blots were imaged with a Molecular Dynamics Storm PhosphorImager and a Packard Instant Imager.
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FIG. 1. DNA products derived from RAP-PCR of total RNA from five independent cultures of D. desulfuricans subsp. aestuarii grown with either hydrogen (lanes 1 to 5) or lactate (lanes 6 to 10) as the electron donor. Arrows indicate cDNA products of differentially transcribed mRNA. A paired control reaction without RT in the first-strand synthesis reaction indicated that no differentially transcribed products were derived from contaminating genomic DNA.
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TABLE 1. DNA sequence homology of differentially transcribed bands obtained by the RAP-PCR procedure
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FIG. 2. Sulfide production in D. desulfuricans subsp. aestuarii throughout the growth curve in mineral medium with 10 mM sulfate added. Growth was monitored spectrophotometrically (optical density at 600 nm [OD600]) with H2 ( ), lactate ( ), or neither () as the electron donorl. Sulfide production was monitored by dimethyl-phenylene diamine assay throughout growth on hydrogen ( ), lactate ( ), or neither electron donor ( ). Yeast extract (0.2%) was included in all media.
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FIG. 3. Northern blot confirmation of differential transcription of dissimilatory bisulfite reductase mRNA. Each lane represents 20 µg of total RNA extracted from three independent cultures of D. desulfuricans subsp. aestuarii grown with neither electron donor (lanes 1 to 3), with hydrogen (lanes 4 to 6), or with lactate (lanes 7 to 10). The blot was incubated with a 32P-labeled RNA probe constructed from a cDNA clone resulting from RAP-PCR and corresponding to the gene sequence for dissimilatory bisulfite reductase.
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TABLE 2. Differential transcription of D. desulfuricans strain Essex 6 redox proteins with either hydrogen or lactate serving as an electron donor
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Increased transcription of the F1F0 ATP synthase and ATP sulfurylase during growth with H2 could not be confirmed by Northern blot analysis. However, we did confirm that dissimilatory bisulfite reductase and adenylylsulfate reductase are transcribed to higher levels in hydrogen-grown cells. It is likely that ATP sulfurylase, one of the four cytoplasmic enzymes involved in sulfate reduction by an eight-electron transfer, and F1F0 ATPase were differentially transcribed but that the Northern blotting was not effective either because of mRNA instability or because of lack of sensitivity. Transcripts with slight levels of differential transcription that RAP-PCR can detect but Northern blots cannot may require more sensitive techniques, such as real-time PCR, for confirmation.
As a follow-up to our findings with dissimilatory bisulfite reductase, we tested whether other redox proteins would be differentially transcribed under conditions of growth with hydrogen. Sequence information for genes encoding several redox proteins was available for D. desulfuricans strain Essex 6. Specific primer pairs were designed for flavodoxin, HmcA, [NiFe] hydrogenase small subunit, and adenylylsulfate reductase b subunit. We were unable to amplify these sequences from D. desulfuricans subsp. aestuarii genomic DNA but were able to amplify and construct probes from Essex 6 DNA. Because the same phenomenon of increased sulfide production during growth on H2 versus lactate occurred in Essex 6 as in the marine strain, other redox proteins can be expected to behave in the same manner in D. desulfuricans Essex 6 as in D. desulfuricans subsp. aestuarii. Northern blots with D. desulfuricans Essex 6 RNA demonstrated that not all putative electron transport-related proteins were transcribed to higher levels when hydrogen was used as an electron donor (Table 2). These results may indicate that certain redox proteins are not involved in hydrogen- or lactate-driven electron transport or that these proteins may not be carrying out rate-limiting reactions. Higher transcription of periplasmic [NiFe] hydrogenase in lactate-grown cells could suggest that this protein plays an important role in metabolism of H2 or in the production of H2 by D. desulfuricans Essex 6 from lactate, lending support to the hydrogen-cycling model. HmcA expression to higher levels during growth on H2 was also demonstrated by Keon et al. (8) through Western blotting.
This study helps in revealing the extent to which different redox proteins play a role in either hydrogen or lactate metabolism. Coupled with previous genetic and biochemical studies, these results may help us come to understand the different pathways employed in the metabolism of lactate or hydrogen in these organisms. From the success of this study, we also feel that RAP-PCR can be applied to other questions of environmental significance, such as the identification of genes that are upregulated in the presence of environmental contaminants.
We thank Chris Bausch and Darren Smalley for providing help with Northern blotting. We also thank Brett Shepard and Michael Gilmore for help with RAP-PCR technique.
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