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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-05-03

AUTHORS

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

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 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. More... »

PAGES

2702-2714

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/ismej.2016.53

DOI

http://dx.doi.org/10.1038/ismej.2016.53

DIMENSIONS

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PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/27137126


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37 CPR lineages
38 Candidate Phyla Radiation
39 Dojkabacteria
40 II/III RubisCO
41 II/III RubisCO diversity
42 II/III RubisCO genes
43 III RubisCO
44 III RubisCO diversity
45 III RubisCO genes
46 Microgenomates
47 Microgenomates (OP11) phyla
48 PER
49 PER form II/III RubisCO
50 Parcubacteria
51 Peregrinibacteria (PER) II/III RubisCO diversity
52 RubisCO deletion strain
53 RubisCO diversity
54 RubisCO genes
55 RubisCO sequences
56 Rubisco
57 Rubisco function
58 WS6
59 WS6 bacterium
60 WS6 phyla
61 addition
62 analysis
63 archaea
64 archaeal form III RubisCO
65 bacteria
66 bacterial photoautotrophic RubisCO deletion strain
67 bacterium
68 bioinformatics analysis
69 capacity
70 context
71 currency
72 deletion strain
73 detection
74 diverse uncultivated phyla
75 diversity
76 diversity of RubisCO
77 form
78 form II/III RubisCO
79 form II/III RubisCO genes
80 form III RubisCO
81 forms of RubisCO
82 function
83 gene transcripts
84 genes
85 genome
86 growth
87 hints
88 identification
89 isolated CPR bacteria
90 lineages
91 metabolic capacity
92 metabolic context
93 metabolic platform
94 metabolism gene transcripts
95 metagenomic studies
96 name Dojkabacteria
97 nucleoside metabolism gene transcripts
98 nucleoside pathway
99 operation
100 organisms
101 organisms hints
102 pathway
103 photoautotrophic RubisCO deletion strain
104 phototrophic growth
105 phyla
106 phyla radiation
107 phylum name Dojkabacteria
108 platform
109 prominent currency
110 radiation
111 ribose
112 sequence
113 simple metabolic platform
114 situ
115 small-celled organisms hints
116 strains
117 study
118 transcripts
119 uncultivated bacteria
120 uncultivated phyla
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