Stepwise pathway for early evolutionary assembly of dissimilatory sulfite and sulfate reduction

Abstract

Microbial dissimilatory sulfur metabolism utilizing dissimilatory sulfite reductases (Dsr) influenced the biochemical sulfur cycle during Earth’s history and the Dsr pathway is thought to be an ancient metabolic process. Here we performed comparative genomics, phylogenetic, and synteny analyses of several Dsr proteins involved in or associated with the Dsr pathway across over 195,000 prokaryotic metagenomes. The results point to an archaeal origin of the minimal DsrABCMK(N) protein set, having as primordial function sulfite reduction. The acquisition of additional Dsr proteins (DsrJOPT) increased the Dsr pathway complexity. Archaeoglobus would originally possess the archaeal-type Dsr pathway and the archaeal DsrAB proteins were replaced with the bacterial reductive-type version, possibly at the same time as the acquisition of the QmoABC and DsrD proteins. Further inventions of two Qmo complex types, which are more spread than previously thought, allowed microorganisms to use sulfate as electron acceptor. The ability to use the Dsr pathway for sulfur oxidation evolved at least twice, with Chlorobi and Proteobacteria being extant descendants of these two independent adaptations.

Microbiota of the sulfur cycle in an extremely contaminated Technosol undergoing pedogenesis: A culture-dependent and metagenomic approach

“…Among them, 14 MAGs also possesed dsrAB, and 9/14 – AprAB and sat proteins, but no DsrD or DsrD-like proteins. Moreover, ten DsrAB-containing bins also encoded DsrEFH, suggesting they can oxidize sulfur compound by both Sox and reverse-Dsr pathways (Neukirchen, Pereira and Sousa, 2023). Over half of SOB group also encoded a variety of organosulfonate monooxygenases and oxidoreductases.…”

“…Dsr pathways(Neukirchen, Pereira and Sousa, 2023). Over half of SOB group also encoded a variety of organosulfonate monooxygenases and oxidoreductases.…”

Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads

“…DsrJOP homologues were analysed for conserved domain architecture using the online webportal for InterPro [79]. Translated protein sequences of the identified dsrJOP genes were aligned with DsrJOP protein sequences, acquired elsewhere [80], using Clustal Omega v1.2.4 with the following parameters: --max-guidetree-iterations=100 --max-hmm-iterations=100 --output-order=tree-order [81]. In addition, the identified DsrP protein sequence was aligned to protein sequences of the NrfD family, acquired elsewhere [82], using Praline with default parameters [82,83].…”

“…Hitherto, only a handful of putative genes from the Dsr pathway have been identified in previous studies, encoding the DsrAB, DsrC, DsrN and DsrMK proteins [41,75]. This could imply that cable bacteria have either a minimal set of Dsr genes, as typically found in ancient sulfate reducers [80], or alternatively, that some Dsr genes have escaped detection (e.g. because of genome incompleteness).…”

“…The putatively homologue of DsrP is predicted to be a membrane protein resembling NrfD with 10 transmembrane helices [108]. Dsr proteins can be phylogenetically categorized as either reductive-type proteins or oxidative-type proteins [80]. To assess which type the putative DsrJOP homologues belong to, we performed a phylogenetic analysis using the expansive dataset of DsrJOP homologues described by Neukirchen et al [80].…”