Dissimilatory sulfate reduction in the archaeon ‘Candidatus Vulcanisaeta moutnovskia’ sheds light on the evolution of sulfur metabolism

Abstract

Extended_Data_Figur e_4.epsError bars represent standard deviations of independent radioisotopic measurement experiments (n = 3).Extended Data Fig.Genes related to sulphate reduction. Extended_Data_Figur e_5.epsThe key sulphate reduction genes from genomes of selected sulphate reducing archaea ("Candidatus V. moutnovskia", Caldivirga sp. Obs2 and A. fulgidus) and bacteria (D. vulgaris Hildenborough and A. degensii) are shown, as well as from genomes of archaea not capable of sulphate reduction (V. distributa, V. souniana, Caldivirga sp. MU80, Ca. Methanodesulfokores washburnensis MDKW and unclassified Aigarchaeota JZ bin 15). Extended Data Fig. Proteomic analysis of the soluble fraction of cells in the binary culture. Extended_Data_Figur e_6.eps Dissimilatory sulphate reduction in archaeon Candidatus Vulcanisaeta moutnovskia sheds light on evolution of sulphur metabolism

DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data

“…The selection was based in one of two criteria. Firstly, a genome was reported in the literature to possess the DsrAB proteins [14,18,45,[56][57][58][59][60][61][62][63][64][65][66][67][68][69][70][71][72]. The presence of DsrAB proteins was validated using the rBBHs of DsrAB proteins following same rBBH strategy as in the complete genome dataset.…”

“…Similarly to AprAB, the Soe complex, is not specific of the oxidative Dsr-pathway, and SoeABC participate in additional sulphur oxidation pathways [42]. In contrast, in dSRP, the Sat, AprAB and Qmo proteins are strictly needed for the activation of sulphate to APS [43] and its reduction to sulphite [44,45].…”

“…However, DsrD is not essential to perform sulphate reduction, albeit its conserved genomic arrangement across dSRP indicates a possible regulatory function in this type of metabolism [53,54]. Some cultured micro-organisms are able to use sulphate as an electron acceptor, without the aid of the DsrD protein [45]. Thus, using this protein as a single marker for the distinction between dSRP from other dSOB might lead to incorrect assignments.…”

“…A second dataset (from now on referred to as the metagenomic dataset) composed of the protein sequences of 193 978 prokaryotic (meta)genomic assemblies and 1900 (meta) genomes belonging to potential new lineages with the ability to use the Dsr-dependent dissimilatory sulphur metabolism [14,18,45,[56][57][58][59][60][61][62][63][64][65][66][67][68][69][70][71][72] was created (Table S3). These additional 1900 (meta)genomes were collected from a survey of recent publications describing potential micro-organisms containing Dsr proteins in the following manner: all assemblies related to the publication BioProject (described or not in the text as a micro-organism having the Dsr pathway) were downloaded and added to the metagenomic dataset, if not already present.…”

“…The combined results of phylogenetic reconstructions, similarity networks and genomic arrangements led to the identification of paralogous proteins, highly similar to enzymes from the Dsr-pathways. A QmoABC complex distinct from known QmoABCs and whose QmoAB subunits are both closely related with the HdrA subunit of the HdrABC complex was recently identified [ 45 ]. For a better orthologous to paralogous distinction, additional HMM profiles were created using representatives of heterodisulphide reductases from methanogens and Proteobacteria [ 89 ], assimilatory Sat as well as the AprAB-like paralogues previously identified in AprAB sequence similarity searches and/or phylogenies [ 45 ].…”