title: RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria.
abstract: 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 CO2to 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.
authors.affiliation: Department of Microbiology, The Ohio State University, Columbus, OH, USA.
authors.forename: Kelly C
authors.initials: KC
authors.lastname: Wrighton
authors.affiliation: Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA.
authors.forename: Cindy J
authors.initials: CJ
authors.lastname: Castelle
authors.affiliation: Department of Microbiology, The Ohio State University, Columbus, OH, USA.
authors.forename: Vanessa A
authors.initials: VA
authors.lastname: Varaljay
authors.affiliation: Department of Microbiology, The Ohio State University, Columbus, OH, USA.
authors.forename: Sriram
authors.initials: S
authors.lastname: Satagopan
authors.affiliation: Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA.
authors.forename: Christopher T
authors.initials: CT
authors.lastname: Brown
authors.affiliation: Department of Microbiology, The Ohio State University, Columbus, OH, USA.|School of Earth Sciences, The Ohio State University, Columbus, OH, USA.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Wilkins
authors.affiliation: Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA.
authors.forename: Brian C
authors.initials: BC
authors.lastname: Thomas
authors.affiliation: Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA.
authors.forename: Itai
authors.initials: I
authors.lastname: Sharon
authors.affiliation: Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
authors.forename: Kenneth H
authors.initials: KH
authors.lastname: Williams
authors.affiliation: Department of Microbiology, The Ohio State University, Columbus, OH, USA.
authors.forename: F Robert
authors.initials: FR
authors.lastname: Tabita
authors.affiliation: Department of Earth and Planetary Science, UC Berkeley, Berkeley, CA, USA.|Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.
authors.forename: Jillian F
authors.initials: JF
authors.lastname: Banfield
mesh_terms: D001105:Archaea / Q000235:genetics / Q000254:growth & development / Q000302:isolation & purification / Q000378:metabolism*; D019843:Archaeal Proteins / Q000235:genetics / Q000378:metabolism*; D001419:Bacteria / Q000235:genetics / Q000254:growth & development / Q000302:isolation & purification / Q000378:metabolism*; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D005285:Fermentation; D056186:Metagenomics; D008969:Molecular Sequence Data; D009705:Nucleosides / Q000378:metabolism*; D010802:Phylogeny; D012273:Ribulose-Bisphosphate Carboxylase / Q000235:genetics
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D009705:Nucleosides; D012273:Ribulose-Bisphosphate Carboxylase