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

Abstract

Current methods in comparative genomic analyses for metabolic potential prediction of proteins involved in, or associated with the Dsr (dissimilatory sulphite reductase)-dependent dissimilatory sulphur metabolism are both time-intensive and computationally challenging, especially when considering metagenomic data. We developed DiSCo, a Dsr-dependent dissimilatory sulphur metabolism classification tool, which automatically identifies and classifies the protein type from sequence data. It takes user-supplied protein sequences and lists the identified proteins and their classification in terms of protein family and predicted type. It can also extract the sequence data from user-input to serve as basis for additional downstream analyses. DiSCo provides the metabolic functional prediction of proteins involved in Dsr-dependent dissimilatory sulphur metabolism with high levels of accuracy in a fast manner. We ran DiSCo against a dataset composed of over 190 thousand (meta)genomic records and efficiently mapped Dsr-dependent dissimilatory sulphur proteins in 1798 lineages across both prokaryotic domains. This allowed the identification of new micro-organisms belonging to Thaumarchaeota and Spirochaetes lineages with the metabolic potential to use the Dsr-pathway for energy conservation. DiSCo is implemented in Perl 5 and freely available under the GNU GPLv3 at https://github.com/Genome-Evolution-and-Ecology-Group-GEEG/DiSCo.

HMS‐S‐S: A tool for the identification of Sulphur metabolism‐related genes and analysis of operon structures in genome and metagenome assemblies

“…HMS-S-S was compared with Psi-BLAST, BLASTp and ProteinOrtho6 in terms of precision and recall in functional annotation (Figure 5). Comparison methods were chosen as they had also been used in the validation of DiSCo (Neukirchen & Sousa, 2021).…”

“…This tool has the advantage of having been created for the classification into orthologue groups of very large numbers of genomes (Lechner et al, 2014). DiSCo is a novel tool that also created HMMs for the detection and classification of sulphur metabolism proteins with a specific focus on the Dsr and Qmo-Apr-Sat pathways (Neukirchen & Sousa, 2021). Sequences for method comparison were taken from the comparison data set.…”

“…Using the comparison data set, the performance of the HMMs generated in our work was assessed by comparison with BLASTp, Psi‐BLAST, ProteinOrtho6 (Lechner et al, 2014) and DiSCo (Neukirchen & Sousa, 2021) (Figure 2c). These methods also served for comparative purposes in previous studies (Neukirchen & Sousa, 2021; Skewes‐Cox et al, 2014). Protein assignments by the respective tool were compared with the originally assigned annotations (cf.…”

“…The unsatisfactory coverage of sulphur metabolism-related proteins by orthologous groups and HMMs is the major cause for the almost exclusive focus of comparative genomic studies on only few well-established metabolic routes, for example, the Dsr (dissimilatory sulphite reductase) pathway (Anantharaman et al, 2018). Recently, a number of additional HMMs became available through a specialized tool for Dsr-dependent sulphur metabolism that now allows for differentiation between oxidative and reductive enzyme types (Neukirchen & Sousa, 2021). However, the presence of reductive or oxidative type enzymes is not strictly correlated with the direction in which the pathway is operated in living cells (Thorup et al, 2017).…”

Sideroxyarcus emersonii gen. nov. sp. nov., a neutrophilic, microaerobic iron- and thiosulfate-oxidizing bacterium isolated from iron-rich wetland sediment

“…The genome sequence was annotated using the rast server version 2.0 [27], the dfast server version 1.2.4 [28] and Prokka version 1.14 [29] with the default settings. The annotation was manually curated based on the results from kegg [30], FeGenie [31] and DiSCo [32].…”