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Cited by 70Microbial Community Ecology and PhysiologyGenomics and Phylogenetic StudiesMetal Extraction and Bioleaching

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

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Neukirchen, Sinje, Pereira, Inês A C, Sousa, Filipa L·2023·The ISME Journal
DOI 10.1038/s41396-023-01477-yPMC PMC10504309
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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.

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  • A deep separation between archaeal and bacterial CbiA/CobB proteins was recently observed in a phylogeny comprising homologous amidases of the different tetrapyrroles present in 2070 assemblies.

    “In addition, a deep separation between archaeal and bacterial CbiA/CobB proteins was also recently observed in a phylogeny comprising homologous amidases of the different tetrapyrroles present in 2070 assemblies [129]”

    From Evidence for corrin biosynthesis in the last universal common ancestor (2025) · cites this paper as [129]

  • A closer inspection of the phylogeny indicated events of interdomain CbiA/CobA transfers with 11 archaeal sequences found in four small clades inside a clade of 1879 bacterial CbiA/CobB proteins.

    “A closer inspection of the phylogeny also indicated events of interdomain CbiA/CobA transfers with 11 archaeal sequences found in four small clades inside a clade of 1879 bacterial CbiA/CobB proteins.”

    From Evidence for corrin biosynthesis in the last universal common ancestor (2025) · cites this paper as [129]

    The Results section on DsrN phylogeny describes bacterial CbiA/CobB proteins and a separate archaeal CbiA clade, but does not report the claimed interdomain transfers or four archaeal clades within a bacterial clade. Searches for the 11 and 1879 sequence counts and for CbiA/CobB transfer did not find those details in our copy. (LLM, conf=0.72)

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Authors
Neukirchen, S., Pereira, I. A. C., & Sousa, F. L.
Affiliations
  • University of Vienna (AT)
  • Instituto de Tecnologia Química e Biológica António Xavier (PT)
Corresponding author
Sousa, Filipa L
ORCID
Venue
The ISME Journal
Publisher
Oxford University Press (OUP)
Published
2023-07-19
Volume
17
Issue
10
Pages
1680-1692
ISSN
  • 1751-7362 (ISSN-L)
  • 1751-7370
DOI
10.1038/s41396-023-01477-y
PMC
PMC10504309
OpenAlex
W4384819184
Cited by
70
References
105
Citations by year
2026: 20 · 2025: 24 · 2024: 23 · 2023: 3
FWCI
11.32
Type
journal article
Language
en
Open access
Licence
Locations
  • The ISME Journal (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) (submittedVersion, other-oa)
Funders
  • European Commission (HORIZON2020)
  • Universität Wien
  • Fundação para a Ciência e a Tecnologia (PTDC/BIA-BQM/29118/2017, PTDC/BIA-MIC/6512/2014)
  • H2020 European Research Council (803768)
Topics
  • Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Engineering › Biomedical Engineering › Metal Extraction and Bioleaching
Keywords
dissimilatory sulfite reductase, dissimilatory sulfate reduction, microbial sulfur metabolism, Archaeoglobus, Chlorobi, Proteobacteria, sulfur oxidation, synteny analysis, comparative genomics, phylogenetic analysis
MeSH terms
Oxidation-Reduction, Phylogeny, Proteins, Sulfates, Sulfites, Sulfur, Oxidoreductases Acting on Sulfur Group Donors, Hydrogensulfite Reductase

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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