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Functional metagenomic selection of ribulose 1, 5‐bisphosphate carboxylase/oxygenase from uncultivated bacteria
Author(s) -
Varaljay Vanessa A.,
Satagopan Sriram,
North Justin A.,
Witte Brian,
Dourado Manuella N.,
Anantharaman Karthik,
Arbing Mark A.,
McCann Shelley Hoeft,
Oremland Ronald S.,
Banfield Jillian F.,
Wrighton Kelly C.,
Tabita F. Robert
Publication year - 2016
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/1462-2920.13138
Subject(s) - rubisco , metagenomics , biology , oxygenase , pyruvate carboxylase , ribulose , enzyme , biochemistry , bacteria , computational biology , genetics , gene
Summary Ribulose 1,5‐bisphosphate carboxylase/oxygenase ( RubisCO ) is a critical yet severely inefficient enzyme that catalyses the fixation of virtually all of the carbon found on E arth. Here, we report a functional metagenomic selection that recovers physiologically active RubisCO molecules directly from uncultivated and largely unknown members of natural microbial communities. Selection is based on CO 2 ‐dependent growth in a host strain capable of expressing environmental deoxyribonucleic acid ( DNA ), precluding the need for pure cultures or screening of recombinant clones for enzymatic activity. Seventeen functional RubisCO ‐encoded sequences were selected using DNA extracted from soil and river autotrophic enrichments, a photosynthetic biofilm and a subsurface groundwater aquifer. Notably, three related form II RubisCOs were recovered which share high sequence similarity with metagenomic scaffolds from uncultivated members of the G allionellaceae family. One of the G allionellaceae RubisCOs was purified and shown to possess CO 2 /O 2 specificity typical of form II enzymes. X ‐ray crystallography determined that this enzyme is a hexamer, only the second form II multimer ever solved and the first RubisCO structure obtained from an uncultivated bacterium. Functional metagenomic selection leverages natural biological diversity and billions of years of evolution inherent in environmental communities, providing a new window into the discovery of CO 2 ‐fixing enzymes not previously characterized.