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College of Marine and Earth Studies and Delaware Biotechnology Institute, University of Delaware, Rm 127 DBI, 15 Innovation Way, Newark, DE 19711, USA
Correspondence
Thomas E. Hanson
tehanson{at}udel.edu
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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Two supplementary tables are available with the online version of this paper.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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; Jung et al., 2000; Wahlund et al., 1991) containing sources of light and reductant, usually reduced sulfur compounds. Although the Chlorobiaceae are thought to be important players in anaerobic sulfur oxidation in aquatic environments, the specific mechanisms and enzymes involved in this process have not been precisely determined. In this work, Chlorobium tepidum was employed as a model system to study sulfur oxidation in the Chlorobiaceae. C. tepidum can be genetically manipulated to produce single mutations (Frigaard & Bryant, 2001; Hanson & Tabita, 2001) but no transposon mutagenesis system has to our knowledge been previously described for this organism. There is also no complementation system yet in place.
C. tepidum can use elemental sulfur (S0), sulfide (H2S/HS–) and thiosulfate (
) as electron donors to support phototrophic growth. While some Chlorobiaceae strains can utilize alternative electron donors such as H2 (Overmann, 2000) and Fe2+ (Heising et al., 1999), growth of C. tepidum is dependent on reduced sulfur compounds. Under phototrophic growth conditions, most Chlorobiaceae are known to oxidize sulfide to elemental sulfur, which accumulates extracellularly (Brune, 1995). After sulfide is depleted, most strains oxidize elemental sulfur to sulfate. In addition, many Chlorobiaceae stains, including C. tepidum, can oxidize thiosulfate to sulfate (Brune, 1995). Little is known about what capacity the Chlorobiaceae have for regulating and integrating the interdependent processes of electron donor oxidation, light harvesting and CO2 fixation.
The complete annotated C. tepidum genome has been used to propose models of sulfur oxidation pathways (Eisen et al., 2002; Hanson & Tabita, 2003). Many of the predicted sulfur oxidation genes in C. tepidum are clustered in groups, which we have termed sulfur islands (Chan et al., 2007). Within these sulfur islands, putative sulfur oxidation genes are interspersed with genes encoding hypothetical and conserved hypothetical proteins of unknown physiological relevance. Sulfur island I is a 32 kb region spanning CT0841 to CT0876 that encodes homologues of the dissimilatory sulfite oxidoreductase complex (Dsr), sulfate adenosyltransferase (Sat), adenosylphosphosulfate reductase (Aps), quinone-interacting membrane oxidoreductase complex (Qmo), thioredoxin reductase, a rhodanese-like protein, and a number of hypothetical and conserved hypothetical proteins. Both the Dsr and Qmo systems have been previously implicated in photosynthetic sulfur oxidation (Pott & Dahl, 1998) and sulfate reduction (Pires et al., 2003), respectively.
How C. tepidum oxidizes thiosulfate remains enigmatic. The genome contains a partial sulfur oxidation (Sox) gene cluster related to that of Paracoccus pantotrophus GB17, whose role in thiosulfate oxidation has been well documented (Friedrich et al., 2001). However, conspicuously absent from the C. tepidum genome are copies of the soxCD genes encoding a sulfur dehydrogenase activity. In fact, soxCD is lacking from all GSB genome sequences collected to date (see Table 4) and from the Chlorobium limicola Pond Mud isolate Sox gene cluster (Verté et al., 2002).
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). These six electrons are 75 % of the total reducing equivalents available from the oxidation of thiosulfate. Two models have been proposed for how C. tepidum harvests these reducing equivalents. That proposed with the genome sequence (Eisen et al., 2002) involves the cleavage of SoxY-bound sulfur to free sulfide followed by periplasmic oxidation of the resulting sulfide via the SoxF flavocytochrome c or SQR. The second, proposed by Hanson & Tabita (2003), invokes transfer of the SoxY-bound sulfur to an unknown low-molecular-mass thiol for subsequent transport and cytoplasmic oxidation.
Here, we report the characterization of the first C. tepidum mutant with a specific defect in thiosulfate-dependent growth, strain C5 (
CT0867–CT0876 : : TnOGm). The mutation responsible for this phenotype is not in the Sox gene cluster, but in a section of sulfur island I, termed SI-I-3, that primarily encodes hypothetical proteins (Fig. 1a) (Chan et al., 2007; Eisen et al., 2002). The phenotype of strain C5 indicates that gene(s) between those encoding the Qmo complex and the SQR homologue in sulfur island I are required for growth on thiosulfate and play a role in acetate assimilation. Cross-genome comparisons with GSB and other bacteria and archaea suggest that the loss of CT0872 is responsible for the thiosulfate oxidation defect while the loss of CT0874 may cause the acetate oxidation defect observed in strain C5. The 256 amino acid polypeptide encoded by CT0872 (30.2 kDa) is annotated as a putative lipoprotein whereas the 159 amino acid product of CT0874 (16.9 kDa) is not currently functionally annotated, suggesting that a novel gene required for anaerobic thiosulfate oxidation is included in this region.
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METHODS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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. Escherichia coli strains were routinely grown in Luria–Bertani (LB) medium at 37 °C (Ausubel et al., 1987).
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), 100 µl vitamin B12 stock (250 µg cyanocobalamin ml–1), 0.5 g KH2PO4, 0.5 g CH3COONH4, 0.4 g NH4Cl and 2.3 g Na2S2O3.5H2O. Component 2 contained 2 g NaHCO3 and 600 ml ddH2O in separate containers. Component 3 contained 0.65 g Na2S.9H2O surface-sterilized with ethanol and 100 ml ddH2O in a small screw-cap bottle.
After sterilization at 121 °C for 20 min, components 1 and 2 were cooled under a 5 % CO2/95 % N2 atmosphere that had been passed through hot copper filings. Component 3 ingredients were mixed while the ddH2O was still hot and sealed. Component 2 was assembled by dissolving the NaHCO3 in the cooled, anoxic ddH2O while bubbling with N2/CO2, followed by bubbling with 100 % CO2 for 20 min. Components 1, 2 and 3 were then combined aseptically followed by the addition of 10 ml sterile, anoxic 1 M BTP pH 7.0 stock. The pH was checked aseptically and, if needed, adjusted to a value of 6.95 with filter-sterilized 2 M Na2CO3 or HCl. Medium was dispensed into sterile 125 ml serum bottles, which were sealed and flushed with the scrubbed 5 % CO2/95 % N2 atmosphere for several minutes. Pf-7-BTP liquid medium was stored at room temperature until use. When made by this method, dissolved sulfide concentrations in the final medium are routinely observed to be 0.6–0.8 mM, which reflects losses by volatilization during medium preparation. Pf-7-BTP was also made with thiosulfate omitted from component 1 and without component 3. This sulfur-free medium was amended with sterile, neutralized, anoxic stock solutions of thiosulfate or sulfide (Overmann, 2000) as needed.
C. tepidum cultures were routinely grown at 47 °C with 20 µmol photons m–2 s–1 of irradiance supplied by 40 W neodymium full-spectrum bulbs (GE Lighting). Irradiance was measured with a quantum PAR sensor attached to a radiometer (Li-COR Biosciences). All cultures were pressurized to 69 kPa with 5 % CO2/95 % N2, which was maintained throughout growth by addition of scrubbed gas as culture aliquots were removed for biomass and sulfur compound determination.
Growth of C. tepidum on CP plates was previously described (Hanson & Tabita, 2001). For all sulfur compound tracking experiments, cells from starter cultures were washed, incubated overnight at 42 °C in sulfur-free Pf-7-BTP medium, and inoculated to a density of 0.5 µg bChl c ml–1. Bacteriochlorophyll (bChl) c and protein concentrations were determined using methanol extraction and the Bradford microassay as previously described (Mukhopadhyay et al., 1999).
Nucleic acid preparation and PCR amplification conditions.
Genomic DNA from C. tepidum was purified either by caesium chloride density-gradient centrifugation or by a commercial kit (Fermentas). Plasmid DNA was harvested from E. coli cultures by a commerical kit (Qiaprep Spin Miniprep kit, Qiagen) or by the boiling lysis DNA extraction method (Ausubel et al., 1987). RNA was purified with a column-based kit purchased from Macherey-Nagel. Trace DNA contamination was removed from RNA samples with TURBO DNA-free (Ambion).
Oligonucleotide primers (Table 2) were purchased from MWG-Biotech. All PCR amplification reactions utilized the FailSafe system (Epicentre). The SI-I-3 PCR product (Fig. 1a
) was amplified in FailSafe buffer G, cloned into pCR-XL-TOPO vector (Invitrogen), and transformed into E. coli TOP10 (Invitrogen) by electroporation. Transposon TnOGm was constructed by amplifying the Gm-resistance gene (aacC1) and the conditional origin of replication (rep) from pTnMod-OGm (Dennis & Zylstra, 1998) using FailSafe buffer C. A 19 bp palindromic mosaic end (ME) sequence (Table 2), recognized by the EZ : : TN transposase, was incorporated into the primers.
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In vitro transposition mutagenesis (IVTM) reactions.
IVTM of TnOGm into the cloned SI-I-3 fragment (see Fig. 1) utilized commercial EZ : : TN transposase (Epicentre). For each reaction, 0.2–0.6 µg of plasmid DNA containing SI-I-3 was used. The reaction was allowed to proceed overnight at 37 °C and the mutagenized plasmid was transformed into E. coli TOP10 (Invitrogen) by electroporation. E. coli clones containing TnOGm were selected on LB plates containing 50 µg kanamycin ml–1 and 10 µg Gm ml–1. Individual colonies were pooled to form an IVTM library, which was stored as a glycerol stock at –70 °C.
Natural transformation of C. tepidum.
Conditions for chromosomal gene inactivation in C. tepidum via natural transformation have been described (Frigaard & Bryant, 2001; Hanson & Tabita, 2001). Modifications for transformation with IVTM libraries follow. Plasmid DNA carrying a mutagenized C. tepidum SI-I-3 fragment was purified from the E. coli library containing IVTM-mutagenized clones. The DNA was linearized, mixed with C. tepidum cells, and incubated on CP plates at 42 °C overnight. Dilutions to 1x10–7 were plated on both nonselective and selective CP plates containing 8 µg Gm ml–1 and incubated for up to 7 days. Colonies were restreaked onto freshly prepared CP-Gm plates as dense patches for secondary selection. After growth, half of the cells in a patch were used to inoculate Pf-7-BTP medium containing 4 µg Gm ml–1. The remaining cells were used to confirm the TnOGm insertion site by PCR. Precise localization of the TnOGm insertion site was determined by sequencing PCR products from mutant strains with a primer directed outward from the left end of TnOGm (Table 2). DNA sequencing was performed at the University of Delaware, College of Agriculture and Natural Resources DNA sequencing core facility.
Quantification of sulfur compounds and acetate by HPLC.
Sulfur compounds were quantified by HPLC as described by Rethmeier et al. (1997) on a class VP HPLC system (Shimadzu Scientific Instruments) equipped with a column oven and UV/visible and fluorescence detectors with the following modifications. Elemental sulfur and monobromobimane-derivatized sulfur compounds (sulfide, thiosulfate, sulfite) were separated on a Prevail C18 5 µm column. Sulfate was determined with an IC AN-1 column using indirect UV detection as previously described (Rethmeier et al., 1997). Thiosulfate and acetate were quantified using a Prevail Organic Acids 5 µm column eluted with 25 mM potassium phosphate buffer, pH 2.5, with UV detection at 210 nm. All columns were purchased from Alltech Associates and the identity of all compounds was confirmed by co-elution with authentic standards.
Data analysis and comparison.
Growth yield data and stoichiometries of sulfur compound consumption and production were calculated from the data in Figs 2, 3 and 4. Values for each of three or four independent cultures were compared between growth conditions or strains by homoscedastic single-tailed t-tests assuming no difference between means and that variance was not constant between sets of values. Tests were conducted in Excel (Microsoft). P-values <0.10 were considered to indicate a significant difference between strains or conditions using this method.
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RESULTS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTSDISCUSSIONREFERENCES |
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(Wahlund et al., 1991). When cultures were incubated under a pressurized headspace of N2/CO2, the pH of the medium routinely rose above 7.2, inhibiting the growth of C. tepidum. Therefore, Pf-7 medium was buffered with BTP (Pf-7-BTP), which maintained a stable pH of 6.9–7.0, improving the reproducibility of C. tepidum growth. BTP does not support the growth of C. tepidum when added to CO2/
-free Pf-7 as the sole carbon source (data not shown).
Application of IVTM to C. tepidum
IVTM with a transposon (TnOGm) derived from pTnModOGm was applied to one subsection of sulfur island I, SI-I-3 (Fig. 1a), encoding homologues of the Desulfovibrio desulfuricans ATCC 27774 QmoABC complex (CT0866–CT0868), a SQR homologue (CT0876), and a number of hypothetical and conserved hypothetical proteins (CT0869–CT0875). TnOGm was utilized in conjunction with a commercial Tn5 transposase to generate transposon insertions in a cloned copy of SI-I-3, generating a library in E. coli containing randomly distributed TnOGm insertions throughout the cloned SI-I-3 fragment. This library was then used to transform C. tepidum, producing a collection of strains carrying TnOGm insertions in SI-I-3, including strains carrying single TnOGm insertions in genes encoding the C. tepidum homologues of QmoB (CT0867 : : TnOGm), QmoC (CT0868 : : TnOGm), and strain C5 (CT0867–CT0876 : : TnOGm, Fig. 1a). Both CT0867 : : TnOGm and CT0868 : : TnOGm mutant strains display very minor phenotypes compared to strain C5 and will be described in detail elsewhere. A C. tepidum strain carrying a single TnOGm insertion in the CT0876 gene was also constructed. The detailed properties of this strain will be described as part of the analysis of the three SQR homologues encoded by the C. tepidum genome (L. K. Chan & T. E. Hanson, unpublished results).
Expression of SI-I-3 genes in wild-type and mutant strain C5
To verify that genes within SI-I-3 were indeed expressed and therefore contribute to C. tepidum's physiology, RT-PCR was used to monitor the expression of qmoA (CT0866), qmoC (CT0868), CT0872 and the sqr-like orthologue (CT0876) in wild-type and mutant strain C5 throughout growth in standard Pf-7-BTP, which contains 9.2 mM thiosulfate and 0.7 mM sulfide as electron donors. In the wild-type strain, transcripts of the qmoA and qmoC homologues were found up to 32 h after inoculation (Fig. 1b), which corresponds to the period of active sulfur oxidation in these cultures (Fig. 2). Sulfide was completely consumed 15 h post-inoculation and elemental sulfur produced from sulfide oxidation was consumed by 24 h (Fig. 2a). Thiosulfate consumption commenced at 15 h and continued until about 40 h post-inoculation, concomitant with sulfate production (Fig. 2b). In contrast, transcripts of CT0872 and the sqr-like orthologue (CT0876) were found in all stages of growth sampled (Fig. 1b), with no obvious connection to sulfur compound dynamics.
RT-PCR was also used to confirm that the gene deletion in strain C5 eliminated the expression of SI-I-3 genes affected by this rearrangement. As expected from the genotype (Fig. 1a), transcripts of CT0868, CT0872 and CT0876 were not detected in strain C5 (Fig. 1c). However, transcripts of qmoA (CT0866) were detected in strain C5, indicating that the partial deletion of qmoB (CT0867) and complete deletion of qmoC (CT0868) did not directly affect the expression of the C. tepidum qmoA homologue.
Growth of wild-type and mutant strain C5
When first isolated, mutant strain C5 exhibited a severe growth rate defect in the presence or absence of Gm selection at 47 °C in Pf-7 medium with no additional buffer (Chan et al., 2007). In contrast, the CT0867 : : TnOGm and CT0868 : : TnOGm mutant strains only displayed strong growth defects in the presence of Gm, suggesting that the Gm resistance marker carried by TnOGm is temperature sensitive (Chan et al., 2007). Therefore, all physiological measurements of C5 were conducted at 47 °C in the absence of Gm selection in well-buffered Pf-7-BTP. The genotype of strains carrying TnOGm insertions examined to date is stable in the absence of Gm selection (L. K. Chan & T. E. Hanson, unpublished results).
In PF-7-BTP with both sulfide and thiosulfate as sulfur and electron donors, C. tepidum wild-type grew with an average doubling time of 2.1 h (Table 3). Mutant strain C5 grew 1.5-fold more slowly, with an average doubling time of 3.2 h (Table 3). When 2.5 mM sulfide was used as the sole sulfur and electron donor, C. tepidum wild-type had a doubling time of 2.3 h, similar to the sulfide+thiosulfate medium, and about 1.7-fold faster than strain C5 growing under the same conditions (Table 3). The total amount of bChl c accumulated by each strain was similar when grown on thiosulfate+sulfide medium versus sulfide alone (Table 3). However, the final yield of biomass (protein) was significantly decreased in sulfide-grown cultures compared to sulfide+thiosulfate, resulting in an increased bChl c : protein ratio (Table 3) for both the wild-type and strain C5. With 12.5 mM thiosulfate as the sole electron donor, C. tepidum wild-type displayed a doubling time of 3.3 h, 1.4-fold slower than cultures grown with sulfide or sulfide+thiosulfate (Table 3). Interestingly, the wild-type accumulated about fourfold higher bChl c when grown on thiosulfate, resulting in the highest bChl c :protein ratio of any growth condition examined (Table 3). Strain C5 was incapable of growth on thiosulfate beyond an initial doubling of biomass (Table 3).
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1 µg protein ml–1. Clearly, TnOGm insertions in genes flanking each side of the deletion in strain C5 have no effect on thiosulfate-dependent growth, suggesting that the loss of genes internal to the deleted region causes the phenotype.
Strain C5 oxidizes sulfide and elemental sulfur, but is deficient for thiosulfate oxidation
When sulfide was provided as the sole reductant for growth, C. tepidum mutant strain C5 oxidized it as well as the wild-type, transiently producing elemental sulfur and eventually producing stoichiometric amounts of sulfate (data not shown). Low, but detectable, amounts of thiosulfate were detected in sulfide-only cultures of both strains, but this was oxidized quickly by the wild-type whereas it persisted in mutant strain C5 (data not shown).
When thiosulfate was provided as the sole reductant, C. tepidum consumed it completely within 48 h (Fig. 3a). No free sulfide was detected during growth of C. tepidum on thiosulfate (data not shown). Elemental sulfur was transiently observed in cultures of the wild-type, and sulfate was the final product of thiosulfate oxidation (Fig. 3b, c). In the wild-type, the maximum concentration of elemental sulfur was 1.2 mM at 25 h, about 5 % of the total sulfur pool originally present in the medium. Extracellular sulfur globules were clearly visible in thiosulfate-oxidizing cultures by microscopy (data not shown). The wild-type produced 1.9 mol sulfate for each mole of thiosulfate oxidized, close to the expected stoichiometry. In contrast to the wild-type, mutant strain C5 did not oxidize thiosulfate (Fig. 3a), nor did it produce elemental sulfur or sulfate (Fig. 3b, c). Sulfur mass balance averaged 91 %±9 % for the wild-type and 96 %±3 % for strain C5 (Fig. 3d). However, wild-type cultures displayed a poor mass balance at the 25 and 48 h time points (88 % and 77 %, respectively). This may indicate that a significant internal pool of sulfur compounds was not detected by the current assay scheme.
Acetate consumption by wild-type and mutant strain C5
Pf-7-BTP contains acetate at a concentration of 6.5 mM and therefore supports mixotrophic growth. Acetate concentrations are routinely measured during analysis of thiosulfate, which led to the serendipitous observation of an acetate assimilation phenotype in strain C5. C. tepidum assimilated acetate in the presence of sulfide+thiosulfate with no noticeable lag, consuming 
75 % during the first 40 h of growth (Fig. 4a). The wild-type also assimilated acetate when grown with either sulfide (Fig. 4b) or thiosulfate (Fig. 4c). In contrast, strain C5 accumulated an additional 1.5 mM acetate during the early stages of growth with thiosulfate+sulfide (Fig. 4a). This accumulation was statistically significant from 10 to 46 h of growth (P<0.10). From a peak of 8 mM acetate at 15 h, strain C5 consumed only about 30 %, reaching a final concentration of 5.6 mM after 60 h of growth (Fig. 4a). When cultures were grown with sulfide, statistically significant differences (P<0.10) in acetate concentrations between the wild-type and strain C5 were observed after 10 h (Fig. 4b), indicating that the mutant did not consume acetate as well as the wild-type under this growth condition. Strain C5 also did not consume acetate when incubated in thiosulfate-containing medium (Fig. 4c), as it did not grow (Fig. 2c).
Analysis of the genomic region deleted in strain C5
The deletion in strain C5 completely eliminates seven ORFs from the genome (Fig. 1a). When compared with other GSB genomes, a similar region was found in Pelodictyon phaeoclathratiforme BU-1 and Chlorobium phaeobacteroides BS-1 (Fig. 5). In the BS-1 strain, this region was found at the end of a scaffold in the draft genome sequence and so the upstream section is implied by light grey shading in Fig. 5, but has not yet been described. The presence of this genomic region is strongly correlated with the ability to oxidize thiosulfate in GSB (Table 4).
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, Table 4). The conserved features of this region are genes encoding sulfate adenyltransferase, adenosine-5'-phosphosulfate reductase, and orthologues of the C. tepidum genes CT0869 and CT0872, which are deleted in strain C5 (Fig. 5). Orthologues of CT0869 and CT0872 are also found amongst sulfate-reducing bacteria and archaea (see Supplementary Table S1, available with the online version of this paper). Any genome that contained an orthologue of CT0869 also contained an orthologue of CT0872, though the converse was not true (Table S1). Genomes encoding an orthologue of CT0872 were searched by TBLASTN with the C. tepidum CT0869 amino acid sequence, but no additional homologues of CT0869 were detected. No obvious functional motifs were detected in CT0869, but the product of CT0872 was weakly similar to PFAM family PF03692 (unknown protein family 0153) and COG0727 (predicted [Fe–S] cluster oxidoreductase). Both families are defined by eight conserved cysteine residues that are also conserved in CT0872.
Also deleted in strain C5 is CT0874, which encodes a protein similar to 3-oxoacyl-acyl-carrier-protein (ACP) synthase IIIs (EC 2.3.1.41, COG0332 and PFAM08545). However, CT0874 encodes only the middle section of a typical FabH enzyme (Davies et al., 2000), and lacks a C-terminal domain (PFAM08541: 2-oxoacyl-ACP synthase III C-terminal) present in bona fide FabH enzymes. A total of 18 proteins that possess a single ACP-synthase III domain in the absence of the C-terminal domain were found to be present in bacterial and eukaryotic genomes (see Supplementary Table S2, available with the online version of this paper). No homologues of CT0874 were detected in other GSB by TBLASTN searches.
The remaining predicted ORFs in this region (CT0870, CT0871 and CT0875) have no significant homology to any other predicted or known ORFs or proteins in current databases. When the SI-I-3 DNA sequence was used in a BLASTX search against the GenBank non-redundant database, an ORF encoding a fragment of anthranilate phosphoribosyltransferase (TrpD, EC 2.4.2.18) was found between CT0872 and CT0874. Presumably a gene model named CT0873 was rejected from this region during annotation because of the presence of CT1609, which encodes a full-length version of TrpD (Eisen et al., 2002).
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DISCUSSION |
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CT0867–CT0876 : : TnOGm). The region deleted in strain C5 is part of a larger cluster termed sulfur island I (Chan et al., 2007) and is not co-localized with the Sox gene cluster (CT1009–CT1027) that is associated with thiosulfate oxidation in other bacteria (Friedrich et al., 2001). Similarly organized regions are found in some GSB and other bacteria, and many of the individual ORFs in this region were found in a number of sulfur-oxidizing and -reducing prokaryote genomes even though they are not co-localized as they are in C. tepidum.
In addition to this observation, this work has provided important basic data on sulfur compound oxidation in C. tepidum. Our data show conclusively that C. tepidum can grow in the absence of sulfide, contradicting reports that sulfide was required for growth of this organism (Wahlund et al., 1991). Furthermore, this report demonstrates the formation of elemental sulfur as a transient intermediate in thiosulfate oxidation in GSB. Elemental sulfur produced by the oxidation of thiosulfate and sulfide was consumed concomitantly with these electron donors.
Two distinct phenotypes were exhibited by mutant strain C5: a specific defect in thiosulfate oxidation that prevented it from growing with thiosulfate as the sole photosynthetic electron donor and a more general defect in acetate assimilation that was found under all growth conditions tested. Two lines of evidence lead us to propose that the thiosulfate oxidation defect of strain C5 is due to the loss of either CT0869 or CT0872, or both genes, in strain C5. First, mutations in genes encoding QmoB (CT0867), QmoC (CT0868) and the SQR homologue (CT0876) in SI-I-3 did not cause a thiosulfate-dependent growth phenotype. Second, homologues of CT0869 and CT0872 are present in the genomes of other thiosulfate-oxidizing GSB. Both genes are also present in two GSB incapable of thiosulfate oxidation, Chlorobium chlorochromatii CaD3 and Chlorobium phaeobacteroides BS-1. However, in these two genomes, these genes are not colocalized in the same genomic region with genes encoding the Qmo complex, suggesting that the overall organization of this gene region may be important to confer thiosulfate oxidation (Table 4). There may also be other genes missing from the CaD3 and Bs-1 genomes, like soxY in the draft BS-1 genome, that prevent these strains from oxidizing thiosulfate.
Evidence for the expression of both CT0872 and CT0869 has been obtained. RT-PCR data reported here indicate that transcripts containing CT0872 are present under standard growth conditions in C. tepidum, and additional RT-PCR experiments indicate that CT0870, CT0871 and CT0872 are present on a single transcript (data not shown). While CT0869 transcription was not assayed here, the CT0869 protein was detected in a proteomic profiling experiment on cytoplasmic extracts of C. tepidum whereas the CT0872 protein was not (Zhou et al., 2007). However, the observed inefficiency of the cytoplasmic profiling experiment for proteins >30 kDa may have prevented detection of the 30.2 kDa CT0872 protein even though it is predicted to have a cytoplasmic localization when examined by PSORTb (http://www.psort.org/psortb/index.html). Alternatively, the failure to observe CT0872 protein may indicate that it is post-translationally modified.
CT0872 seems the most likely candidate for a direct role in thiosulfate oxidation based on its wider distribution in other thiosulfate-oxidizing bacteria, like T. denitrificans (Table 4), and other sulfur-oxidizing and -reducing bacteria and archaea (Table S1). The weak homology of the CT0872 protein to predicted [Fe–S] oxidoreductases (PF03692 and COG0727), based on eight conserved cysteines, may indicate that it participates in redox reactions via bound metals or [Fe–S] clusters, but this remains to be experimentally determined. The T. denitrificans orthologue of CT0872, Tbd0871, was found to be highly expressed during both aerobic and anaerobic growth with thiosulfate as the electron donor (Beller et al., 2006), along with the genes encoding sulfate adenyltransferase and adenosine-5'-phosphosulfate reductase. Like C. tepidum and all other GSB, T. denitrificans lacks genes encoding a SoxCD complex, which is required for complete thiosulfate oxidation in P. pantotrophus GB17.
In the purple sulfur bacterium Allochromatium vinosum, genes of the dsr cluster have been implicated in the oxidation of periplasmic elemental sulfur, formed as an intermediate during the oxidation of thiosulfate. A. vinosum, like C. tepidum, lacks genes encoding the SoxCD sulfur dehydrogenase, and it has been suggested that elemental sulfur is an intermediate of thiosulfate oxidation in strains lacking SoxCD. C. tepidum was shown here to produce limited quantities of elemental sulfur during thiosulfate oxidation, in agreement with the lack of SoxCD. However, it is clear that the dsr genes are not required for photolithotrophic growth on either sulfide or thiosulfate in A. vinosum (Pott & Dahl, 1998). This strongly contrasts with the phenotype of strain C5, which is completely incapable of thiosulfate-dependent growth. Further experiments on growth-independent thiosulfate turnover in this strain will reveal whether or not C5 accumulates intermediates. The existence of additional intermediates in thiosulfate oxidation in C. tepidum is suggested by the observation that C. tepidum does not display a good sulfur mass balance in the late stages of growth on thiosulfate as the sole electron donor (Fig. 3d).
Another key difference between A. vinosum and C. tepidum is the formation of periplasmic elemental sulfur globules in A. vinosum, which is dependent on the sulfur globule proteins encoded by sgpA, sgpB and sgpC (Prange et al., 2004). The formation of these globules appears to be required for photolithotrophic growth, as indicated by the inability of an A. vinosum sgpBC double mutant to grow on sulfide or thiosulfate (Prange et al., 2004). C. tepidum accumulates elemental sulfur extracellularly, does not have sgp gene homologues, and yet grows perfectly well on thiosulfate and sulfide. This indicates that key differences must exist between these strains in how elemental sulfur is formed and oxidized. Strain C5 appears to consume elemental sulfur produced from sulfide oxidation normally, so we conclude that the mutation in strain C5 has not affected any putative dsr-dependent elemental sulfur oxidation capacity, but rather the entry of thiosulfate-derived sulfur into such a pathway.
Regarding the acetate assimilation defect, we propose that CT0874 provides a mechanism for C. tepidum to buffer or retain acetate intracellularly. This is consistent with the observation that strain C5 accumulates acetate in culture supernatants during growth with thiosulfate+sulfide under both mixotrophic (Fig. 4a) and autotrophic (data not shown) conditions.
While it is a formal possibility that one or more of the genes deleted in strain C5 is a regulatory factor that controls thiosulfate oxidation or acetate oxidation, we feel this is unlikely. None of the genes in this region display any similarity to known regulatory genes or contain recognized regulatory motifs such as DNA-binding domains or protein–protein interaction domains (data not shown). To further examine this point, we are developing RT-PCR primers for Sox genes and those encoding key steps in acetate assimilation to determine if these genes are expressed normally in strain C5. When compared to the wild-type strain by SDS-PAGE, strain C5 displays no obvious protein profile differences (data not shown) that might suggest severe alterations in global regulation as observed in the 
: : RLP mutant strain (Hanson & Tabita, 2001, 2003).
While our results are suggestive of the function proposed for specific gene products above, they are obviously not conclusive due to the lack of a plasmid-based complementation system in C. tepidum. Experiments are under way to directly test the proposed functions for CT0872 and CT0874 by the construction and phenotypic characterization of C. tepidum strains carrying single TnOGm insertions in these genes. Together with our earlier report (Chan et al., 2007), the data reported here indicate that IVTM is an extremely useful technique for characterizing genomic regions of interest in C. tepidum.
Finally, the data suggest that C. tepidum dynamically regulates light harvesting in response to the electron donor provided. Cells grown on sulfide+thiosulfate displayed the lowest specific bChl c content, with sulfide-grown and thiosulfate-grown cells displaying 4-fold and 10-fold increases, respectively. Temperature and light intensity also affect photosynthetic antenna structure and function in wild-type cells while strain C5 appears chronically affected, as will be detailed elsewhere (R. M. Morgan-Kiss, L. K. Chan, T. S. Weber & T. E. Hanson, unpublished).
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ACKNOWLEDGEMENTS |
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Edited by: G. Muyzer
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Received 30 August 2007;
revised 18 November 2007;
accepted 23 November 2007.
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) and sulfate (
). The data are means and standard errors of three or four independent replicates.
) and SI-I-3 mutant strain C5 (
) grown in Pf-7-BTP with 12.5 mM thiosulfate. Concentrations of thiosulfate (a), elemental sulfur (b) and sulfate (c) were measured as described in Methods and the total sulfur recovery (d) was expressed as a percentage of the total of all sulfur compounds detected at time 0. The data are means and standard errors of three or four independent replicates.
