Limits...
Permanent draft genome of Thermithiobaclillus tepidarius DSM 3134 T , a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia

View Article: PubMed Central - PubMed

ABSTRACT

Thermithiobacillus tepidarius DSM 3134T was originally isolated (1983) from the waters of a sulfidic spring entering the Roman Baths (Temple of Sulis-Minerva) at Bath, United Kingdom and is an obligate chemolithoautotroph growing at the expense of reduced sulfur species. This strain has a genome size of 2,958,498 bp. Here we report the genome sequence, annotation and characteristics. The genome comprises 2,902 protein coding and 66 RNA coding genes. Genes responsible for the transaldolase variant of the Calvin-Benson-Bassham cycle were identified along with a biosynthetic horseshoe in lieu of Krebs’ cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). Metalloresistance genes involved in pathways of arsenic and cadmium resistance were found. Evidence of horizontal gene transfer accounting for 5.9 % of the protein-coding genes was found, including transfer from Thiobacillus spp. and Methylococcus capsulatus Bath, isolated from the same spring. A sox gene cluster was found, similar in structure to those from other Acidithiobacillia – by comparison with Thiobacillus thioparus and Paracoccus denitrificans, an additional gene between soxA and soxB was found, annotated as a DUF302-family protein of unknown function. As the Kelly-Friedrich pathway of thiosulfate oxidation (encoded by sox) is not used in Thermithiobacillus spp., the role of the operon (if any) in this species remains unknown. We speculate that DUF302 and sox genes may have a role in periplasmic trithionate oxidation.

No MeSH data available.


Structure of the sox cluster in T. tepidarius and other chemolithoautotrophic Proteobacteria. A reference sox operon encoding the Kelly-Friedrich pathway of thiosulfate oxidation from Paracoccus denitrificans ATCC 17741T (Alphaproteobacteria) is given, showing soxXYZABCDEF genes and intergenic spacers, against gene clusters from T. tepidarius DSM 3134T, A. thiooxidans ATCC 19377T and A. caldus ATCC 51756T (the only sulfur-oxidising Acidithiobacillus spp.) of the Acidithiobacillia; Thiohalorhabdus denitrificans DSM 15699T (Gammaproteobacteria) and Thiobacillus thioparus DSM 505T (Betaproteobacteria). The DUF302-family hypothetical protein gene is indicated where present. It is worth noting that P. denitrificans and T. thioparus do not grow on trithionate and that thiosulfate oxidation in Thermithiobacillus and Thiobacillus has been unequivocally shown not to proceed via the periplasmic Kelly-Friedrich oxidation pathway and instead occurs via tetrathionate as an intermediate, which is then oxidized to sulfate in the cytoplasm (the Kelly-Trudinger pathway [32, 33]). The highly conserved soxXYZAB cluster occurs in all of the genomes examined and the DUF302 gene appears highly conserved in the Acidithiobacillia. The function is as-yet unknown, as is that of the sox genes in these Kelly-Trudinger pathway organisms. Analysis of conserved domains indicates that DUF302 may form a homodimer
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC5037610&req=5

Fig3: Structure of the sox cluster in T. tepidarius and other chemolithoautotrophic Proteobacteria. A reference sox operon encoding the Kelly-Friedrich pathway of thiosulfate oxidation from Paracoccus denitrificans ATCC 17741T (Alphaproteobacteria) is given, showing soxXYZABCDEF genes and intergenic spacers, against gene clusters from T. tepidarius DSM 3134T, A. thiooxidans ATCC 19377T and A. caldus ATCC 51756T (the only sulfur-oxidising Acidithiobacillus spp.) of the Acidithiobacillia; Thiohalorhabdus denitrificans DSM 15699T (Gammaproteobacteria) and Thiobacillus thioparus DSM 505T (Betaproteobacteria). The DUF302-family hypothetical protein gene is indicated where present. It is worth noting that P. denitrificans and T. thioparus do not grow on trithionate and that thiosulfate oxidation in Thermithiobacillus and Thiobacillus has been unequivocally shown not to proceed via the periplasmic Kelly-Friedrich oxidation pathway and instead occurs via tetrathionate as an intermediate, which is then oxidized to sulfate in the cytoplasm (the Kelly-Trudinger pathway [32, 33]). The highly conserved soxXYZAB cluster occurs in all of the genomes examined and the DUF302 gene appears highly conserved in the Acidithiobacillia. The function is as-yet unknown, as is that of the sox genes in these Kelly-Trudinger pathway organisms. Analysis of conserved domains indicates that DUF302 may form a homodimer

Mentions: Two pairs of genes encoding ribulose-1,6-bisphosphate carboxylase (RuBisCO) could be identified, each comprising a large and small subunit gene. One pair is found close to cbbO and cbbQ genes, with no other cbb genes closeby – this is consistent with Acidithiobacillus spp. and other obligate chemolithoautotrophs and indicates a Form IAq RuBisCO. The other pair is found close to cbb genes and in that sense is perhaps more similar to Form II RuBisCO [26]. Metalloresistance genes including those for arsenite efflux and arsenate reductase (arsB and arsC, respectively) were identified along with those implicated in tellurite, cadmium, cobalt, zinc, copper and silver resistance. Sulfur-oxidation genes are obviously of paramount interest in an obligate chemolithoautotroph, however, a number of proposed enzymes of sulfur metabolism have no genes identified thus far. It is known that the Acidithiobacillia [1, 2, 4–6] do not use the Kelly-Friedrich or “Sox” pathway of thiosulfate oxidation, and instead oxidise thiosulfate to tetrathionate via a poorly understood dehydrogenase – more than one form of which may exist. Some Kelly-Friedrich pathway genes are present in the genome and these are given in Fig. 3, showing comparison with those from other organisms that do not use the Kelly-Friedrich pathway versus one (Paracoccus denitrificans) that does. It can be seen from Fig. 3 that the non-Kelly-Friedrich organisms lack the soxC and soxD genes that are involved in a 6-electron capture during thiosulfate oxidation and all contain a gene encoding DUF302-family protein of unknown function 191 amino acids in length (G579DRAFT_01426 in T. tepidarius). Assuming these proteins are found in the periplasm of T. tepidarius as they are in Paracoccus spp., they could play a role in trithionate or higher polythionate oxidation (tetrathionate being oxidized solely in the cytoplasm [6]. The DUF302 protein of T. tepidarius would have a mass of 20.6 kDa based on the amino acyl sequence but contains a potential dimerization domain, so could be 41.2 kDa. It is worth noting that the periplasmic trithionate hydrolase (EC 3.12.1.1, gene unknown) of Acidiphilium acidophilum was 35 kDa [27].Fig. 3


Permanent draft genome of Thermithiobaclillus tepidarius DSM 3134 T , a moderately thermophilic, obligately chemolithoautotrophic member of the Acidithiobacillia
Structure of the sox cluster in T. tepidarius and other chemolithoautotrophic Proteobacteria. A reference sox operon encoding the Kelly-Friedrich pathway of thiosulfate oxidation from Paracoccus denitrificans ATCC 17741T (Alphaproteobacteria) is given, showing soxXYZABCDEF genes and intergenic spacers, against gene clusters from T. tepidarius DSM 3134T, A. thiooxidans ATCC 19377T and A. caldus ATCC 51756T (the only sulfur-oxidising Acidithiobacillus spp.) of the Acidithiobacillia; Thiohalorhabdus denitrificans DSM 15699T (Gammaproteobacteria) and Thiobacillus thioparus DSM 505T (Betaproteobacteria). The DUF302-family hypothetical protein gene is indicated where present. It is worth noting that P. denitrificans and T. thioparus do not grow on trithionate and that thiosulfate oxidation in Thermithiobacillus and Thiobacillus has been unequivocally shown not to proceed via the periplasmic Kelly-Friedrich oxidation pathway and instead occurs via tetrathionate as an intermediate, which is then oxidized to sulfate in the cytoplasm (the Kelly-Trudinger pathway [32, 33]). The highly conserved soxXYZAB cluster occurs in all of the genomes examined and the DUF302 gene appears highly conserved in the Acidithiobacillia. The function is as-yet unknown, as is that of the sox genes in these Kelly-Trudinger pathway organisms. Analysis of conserved domains indicates that DUF302 may form a homodimer
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC5037610&req=5

Fig3: Structure of the sox cluster in T. tepidarius and other chemolithoautotrophic Proteobacteria. A reference sox operon encoding the Kelly-Friedrich pathway of thiosulfate oxidation from Paracoccus denitrificans ATCC 17741T (Alphaproteobacteria) is given, showing soxXYZABCDEF genes and intergenic spacers, against gene clusters from T. tepidarius DSM 3134T, A. thiooxidans ATCC 19377T and A. caldus ATCC 51756T (the only sulfur-oxidising Acidithiobacillus spp.) of the Acidithiobacillia; Thiohalorhabdus denitrificans DSM 15699T (Gammaproteobacteria) and Thiobacillus thioparus DSM 505T (Betaproteobacteria). The DUF302-family hypothetical protein gene is indicated where present. It is worth noting that P. denitrificans and T. thioparus do not grow on trithionate and that thiosulfate oxidation in Thermithiobacillus and Thiobacillus has been unequivocally shown not to proceed via the periplasmic Kelly-Friedrich oxidation pathway and instead occurs via tetrathionate as an intermediate, which is then oxidized to sulfate in the cytoplasm (the Kelly-Trudinger pathway [32, 33]). The highly conserved soxXYZAB cluster occurs in all of the genomes examined and the DUF302 gene appears highly conserved in the Acidithiobacillia. The function is as-yet unknown, as is that of the sox genes in these Kelly-Trudinger pathway organisms. Analysis of conserved domains indicates that DUF302 may form a homodimer
Mentions: Two pairs of genes encoding ribulose-1,6-bisphosphate carboxylase (RuBisCO) could be identified, each comprising a large and small subunit gene. One pair is found close to cbbO and cbbQ genes, with no other cbb genes closeby – this is consistent with Acidithiobacillus spp. and other obligate chemolithoautotrophs and indicates a Form IAq RuBisCO. The other pair is found close to cbb genes and in that sense is perhaps more similar to Form II RuBisCO [26]. Metalloresistance genes including those for arsenite efflux and arsenate reductase (arsB and arsC, respectively) were identified along with those implicated in tellurite, cadmium, cobalt, zinc, copper and silver resistance. Sulfur-oxidation genes are obviously of paramount interest in an obligate chemolithoautotroph, however, a number of proposed enzymes of sulfur metabolism have no genes identified thus far. It is known that the Acidithiobacillia [1, 2, 4–6] do not use the Kelly-Friedrich or “Sox” pathway of thiosulfate oxidation, and instead oxidise thiosulfate to tetrathionate via a poorly understood dehydrogenase – more than one form of which may exist. Some Kelly-Friedrich pathway genes are present in the genome and these are given in Fig. 3, showing comparison with those from other organisms that do not use the Kelly-Friedrich pathway versus one (Paracoccus denitrificans) that does. It can be seen from Fig. 3 that the non-Kelly-Friedrich organisms lack the soxC and soxD genes that are involved in a 6-electron capture during thiosulfate oxidation and all contain a gene encoding DUF302-family protein of unknown function 191 amino acids in length (G579DRAFT_01426 in T. tepidarius). Assuming these proteins are found in the periplasm of T. tepidarius as they are in Paracoccus spp., they could play a role in trithionate or higher polythionate oxidation (tetrathionate being oxidized solely in the cytoplasm [6]. The DUF302 protein of T. tepidarius would have a mass of 20.6 kDa based on the amino acyl sequence but contains a potential dimerization domain, so could be 41.2 kDa. It is worth noting that the periplasmic trithionate hydrolase (EC 3.12.1.1, gene unknown) of Acidiphilium acidophilum was 35 kDa [27].Fig. 3

View Article: PubMed Central - PubMed

ABSTRACT

Thermithiobacillus tepidarius DSM 3134T was originally isolated (1983) from the waters of a sulfidic spring entering the Roman Baths (Temple of Sulis-Minerva) at Bath, United Kingdom and is an obligate chemolithoautotroph growing at the expense of reduced sulfur species. This strain has a genome size of 2,958,498 bp. Here we report the genome sequence, annotation and characteristics. The genome comprises 2,902 protein coding and 66 RNA coding genes. Genes responsible for the transaldolase variant of the Calvin-Benson-Bassham cycle were identified along with a biosynthetic horseshoe in lieu of Krebs’ cycle sensu stricto. Terminal oxidases were identified, viz. cytochrome c oxidase (cbb3, EC 1.9.3.1) and ubiquinol oxidase (bd, EC 1.10.3.10). Metalloresistance genes involved in pathways of arsenic and cadmium resistance were found. Evidence of horizontal gene transfer accounting for 5.9 % of the protein-coding genes was found, including transfer from Thiobacillus spp. and Methylococcus capsulatus Bath, isolated from the same spring. A sox gene cluster was found, similar in structure to those from other Acidithiobacillia – by comparison with Thiobacillus thioparus and Paracoccus denitrificans, an additional gene between soxA and soxB was found, annotated as a DUF302-family protein of unknown function. As the Kelly-Friedrich pathway of thiosulfate oxidation (encoded by sox) is not used in Thermithiobacillus spp., the role of the operon (if any) in this species remains unknown. We speculate that DUF302 and sox genes may have a role in periplasmic trithionate oxidation.

No MeSH data available.