A presence of sigma 54 transcryptional regulator has also previously been shown in the TcDH operon of thiocyanate-oxidizing members of the genus Thioalkalivibrio Berben et al. Thiocyanate dehydrogenase has a Tat signal peptide and is exported to periplasm with twin-arginine translocation pathway. This pathway is used to transfer a folded protein to the periplasm.
The reason for exporting an enzyme in 3D conformation is in acquiring a complex multi-atom cofactor in the cytoplasm Lee et al. That is why copper ions need to be transferred into cytoplasm. Also, bacteria need to supply TcDH synthesis with sufficient amount of copper. These genes belong to Cus system, which is known to be involved in copper homeostasis in Escherichia coli.
Three genes are located further upstream to TcDH Figure 5 with almost no gaps, indicating a possibility of their simultaneous expression and a common function. The first two of them encode membrane proteins. The latter are part of CusCBA copper transport system. CusA encodes copper membrane transporter efflux pump.
This protein is reported to transport Cu I and Ag I ions across inner membrane in both directions Long et al. Considering copper dependence of TcDH, these genes are more likely to be Cus genes homologs. Based on that, we can assume that the other genes of the operon are also related to copper transport. One of them should be an outer member protein, another — a fusion protein, bridging this protein with CusA across periplasm.
The gene adjacent to cusA encodes a large amino acid protein which was expected to be CusC, however, pairwise alignments with known CusC showed poor results. According to phi-blast search results and InterProScan classification this is a homolog of a histidine kinase. This transmembrane domain was also detected by InterProScan and confirmed by secondary structure prediction with JPred. The transmembrane domain of this protein is not assigned to any protein family. Multiple alignment shows presence of highly conserved methionines and histidines in this domain, that are typical protein ligands for copper ions Rubino and Franz, Residues — were determined as GAF-like domain, and — as a histidine kinase family.
The remaining histidine kinase domain can perform various functions. In several studies Ag and Cu transport activity was reported for proteins with this domain Gudipaty and McEvoy, ; Affandi et al. Overall, we can say that this is a membrane-bound protein with a putative copper transport function same function as cusC. According to superfamily description, these proteins form a bridge between inner and outer membrane transporters. In case of these organisms, if one cusB gene is present in a genome, it is always followed by the second cusB. Moreover, this gene pair was always preceded by cusA gene.
Despite of that, the proteins have a number of similarities, and the most striking one is that they apparently belong to the same protein family, determined by InterProScan. Both have a signal peptide at 20—25 AA. Prediction analysis with JPred 4 demonstrated a very similar secondary structure pattern. Most of these strands have a lot of conserved residues, while other parts of the sequence are more variable.
These similarities might be taken as evidence of a common function of both proteins, but the reason of such duplication is unclear. Figure 6.
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Secondary structure of each protein was modeled by Jpred 4. Beta-strands and alpha helices are shown by green arrows and red cylinders, respectively. However, these genes were not found in halophilic Thiohalobacter and Guyparkeria , while obviously being substituted for another type of copper transport system Cus , which might have something to do with the copper availability difference at neutral pH 7 and highly alkaline pH 10 growth conditions of halophilic and haloalkaliphilic SOB species, respectively. Recently, a genome announcement has been published Oshiki et al.
While such values in general are typical of closely related prokaryotes, the publishing of an organism with the same species name can not be considered as legal before a full polyphasic taxonomic description is provided. Therefore, here we provide only a brief comparison of the sulfur oxidation related genes present in the genome of this bacterium, since none of the genomic information is yet backed up by the published phenotypical data.
Comparative genome analysis of halophilic SOB from two distant clusters of Gammaproteobacteria capable of thiocyanate oxidation by the cyanate pathway demonstrated a remarkable difference in their mainstream sulfur oxidation pathway. While the Thiohalobacter , a member of Chromatiales , is oxidizing zero-valent sulfur using the rDSR pathway, common for anaerobic SOB, and thiosulfate by an incomplete Sox pathway, common to most of the aerobic gammaproteobacterial SOB, the Guyparkeria SCN-R1 is using complete Sox pathway, normally present in aerobic alpha- and betaproteobacteria.
On the other hand, the system responsible for thiocyanate oxidation to cyanate and zero-valent sulfur is very similar in both organisms with the central role of TcDH homologous to the one present in the genus Thioalkalivibrio. It might be speculated, that this can be related to the different pH environment. ST and TT performed bioinformatic analysis of the thiocyanate-related metabolism. DS performed the microbiological experiments and bioinformatic analysis of central metabolism.
GM performed the phylogenetic and genome analyses and general coordination of the manuscript writing. VP participated in data analysis and writing the manuscript.
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. We thank Tom Berben for helping with extended phylogenetic analysis of a SoeA-like protein and Enzo Messina for performing whole genome comparison of Thiohalobacter strains. Abascal, F. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21, — Google Scholar. Affandi, T.
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Bioinformatics 28, — Punta, M. Membrane protein prediction methods. Methods 41, — Quast, C. Rabus, R. A wide selection of species was selected, from multiple branches of the tree of life; e. Some landplants were also added as reference. Focused on dicot species, but with some others as reference organisms. PLAZA 3. Focused on monocot species, but with some others as reference organisms. This version was quickly discontinued with the release of the TAIR10 release of Arabidopsis thaliana.
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