RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria

Wrighton, Kelly C.; Castelle, Cindy J.; Varaljay, Vanessa A.; Satagopan, Sriram; Brown, Christopher T.; Wilkins, Michael J.; Thomas, Brian C.; Sharon, Itai; Williams, Kenneth H.; Tabita, F. Robert; Banfield, Jillian F.

doi:10.1038/ismej.2016.53

Title: RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria

Journal Article · Tue May 03 00:00:00 EDT 2016 · The ISME Journal

DOI:https://doi.org/10.1038/ismej.2016.53· OSTI ID:1377559

Wrighton, Kelly C. ^[1]; Castelle, Cindy J. ^[2]; Varaljay, Vanessa A. ^[1]; Satagopan, Sriram ^[1]; Brown, Christopher T. ^[2]; Wilkins, Michael J. ^[1]; Thomas, Brian C. ^[2]; Sharon, Itai ^[2]; Williams, Kenneth H. ^[3]; Tabita, F. Robert ^[1]; Banfield, Jillian F. ^[2]

The Ohio State Univ., Columbus, OH (United States)
Univ. of California, Berkeley, CA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Metagenomic studies recently uncovered form II/III RubisCO genes, originally thought to only occur in archaea, from uncultivated bacteria of the candidate phyla radiation (CPR). There are no isolated CPR bacteria and these organisms are predicted to have limited metabolic capacities. Here we expand the known diversity of RubisCO from CPR lineages. We report a form of RubisCO, distantly similar to the archaeal form III RubisCO, in some CPR bacteria from the Parcubacteria (OD1), WS6 and Microgenomates (OP11) phyla. In addition, we significantly expand the Peregrinibacteria (PER) II/III RubisCO diversity and report the first II/III RubisCO sequences from the Microgenomates and WS6 phyla. To provide a metabolic context for these RubisCOs, we reconstructed near-complete ( > 93%) PER genomes and the first closed genome for a WS6 bacterium, for which we propose the phylum name Dojkabacteria. Genomic and bioinformatic analyses suggest that the CPR RubisCOs function in a nucleoside pathway similar to that proposed in Archaea. Detection of form II/III RubisCO and nucleoside metabolism gene transcripts from a PER supports the operation of this pathway in situ. We demonstrate that the PER form II/III RubisCO is catalytically active, fixing CO₂ to physiologically complement phototrophic growth in a bacterial photoautotrophic RubisCO deletion strain. We propose that the identification of these RubisCOs across a radiation of obligately fermentative, small-celled organisms hints at a widespread, simple metabolic platform in which ribose may be a prominent currency.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1377559

Journal Information:: The ISME Journal, Vol. 10, Issue 11; ISSN 1751-7362

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 65 works

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