The Thermotoga clade (excluding Tt. lettingae and Tt. thermarum) contains both B12-independent and -dependent forms of methionine synthase and ribonucleotide reductase ( online). The loss of the cobinamide salvage genes in the Thermotoga clade may be due to the use of B12-independent enzymes by these organisms. Methionine synthase () and ribonucleotide reductase () are the only B12-dependent enzymes in the Thermotoga clade, whereas the other clades have multiple B12-binding proteins suggesting a possible need for B12 by those species ( online). With few or no B12-binding domain proteins, selection pressure to maintain a B12 biosynthesis pathway should diminish. This relaxed selection pressure may have allowed for loss of the pathway. We have successfully grown Thermotoga species (Tt. maritima, Tt. sp. RQ2, Tt. sp. cell2, Tt. naphthophila, Tt. neapolitana, and Tt. petrophila) without the addition of B12 on B12-free media, showing B12 is not essential for growth. These media were determined to be B12 free using the Lactobacillus bioassay (; ; ). Both B12-dependent methionine synthase () and ribonucleotide reductase () from T. maritima have been previously shown in vitro to require B12 as a cofactor for activity, and the expression data of btuF (BtuFCD transporter) suggests that B12 is imported into the cell (). This suggests that B12 is not essential but can be utilized in this clade.
Putative B12 riboswitches were identified near four gene clusters linked to B12 metabolism. The phylogenetic distribution of these clusters within the Thermotogales is depicted in . The evolutionary histories of these clusters were traced by ancestral state reconstruction using maximum parsimony and maximum likelihood () models. These analyses suggest the cobinamide salvage pathway was present in the ancestor of the Thermotogales and was lost in the lineages leading to the Thermotoga (excluding Tt. lettingae and Tt. thermarum), Petrotoga mobilis, and Mesotoga prima (). The reconstructions also suggest that the corrinoid synthesis gene cluster was gained on the branch leading to the Thermosipho lineage. Both reconstructions support the SucCoA synthetase gene cluster as either being acquired twice, once at the base of the Thermosipho/Fervidobacterium clade and once in Tt. lettingae, or perhaps gained once by one of the clades and then transferred to the other.
De novo and salvage pathways of DNA synthesis in …
The genes that encode de novo synthesis () of B12 that are thought to be subject to B12 riboswitch regulation were tested for expression when cells were grown with and without B12. In the presence of B12, the corrinoid synthesis and cobinamide salvage genes are down-regulated (). This is consistent with findings in other organisms (; ) and suggests that these genes allow Thermosipho species to produce B12 and are regulated at the transcriptional level. An open reading frame (ORF) adjacent to cbiO in the corrinoid synthesis island was also tested, and its expression was down-regulated along with the other genes (). Although the function of this gene is unknown, it has a predicted ATP-binding domain and has homologs present within the cobinamide salvage island of F. nodosum ( online). The ORF is also found within gene clusters related to B12 synthesis in other genomes (e.g., Thermodesulfovibrio yellowstonii and Archaeoglobus fulgidus). This suggests that this ORF is related to B12 synthesis/cobinamide salvage.
Pentose phosphate pathway - Wikipedia
The biosynthesis of purine and pyrimidine nucleotides takes place over de novo synthetic pathways from small molecules and by salvage pathways from preformed purine or pyrimidine bases or nucleosides. The pathways of de novo synthesis are the same in animals and microorganisms. Salvage pathways are considerably more energy-efficient than de novo pathways, which require 5 (pyrimidine) or 6 (purine) moles of ATP for each mole of nucleotide produced.
Purine and Pyrimidine Metabolism - EHSL
The availability of genome sequences of Thermotogales species from across the order allows an examination of the evolutionary origins of phenotypic characteristics in this lineage. Several studies have shown that the Thermotogales have acquired large numbers of genes from distantly related lineages, particularly Firmicutes and Archaea. Here, we report the finding that some Thermotogales acquired the ability to synthesize vitamin B12 by acquiring the requisite genes from these distant lineages. Thermosipho species, uniquely among the Thermotogales, contain genes that encode the means to synthesize vitamin B12 de novo from glutamate. These genes are split into two gene clusters: the corrinoid synthesis gene cluster, that is unique to the Thermosipho and the cobinamide salvage gene cluster. The corrinoid synthesis cluster was acquired from the Firmicutes lineage, whereas the salvage pathway is an amalgam of bacteria- and archaea-derived proteins. The cobinamide salvage gene cluster has a patchy distribution among Thermotogales species, and ancestral state reconstruction suggests that this pathway was present in the common Thermotogales ancestor. We show that Thermosipho africanus can grow in the absence of vitamin B12, so its de novo pathway is functional. We detected vitamin B12 in the extracts of T. africanus cells to verify the synthetic pathway. Genes in T. africanus with apparent B12 riboswitches were found to be down-regulated in the presence of vitamin B12 consistent with their roles in B12 synthesis and cobinamide salvage.