Functional metagenomic selection of RubisCOs from uncultivated bacteria

Environmental Microbiology
By: , and 

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Abstract

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 Earth. 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 CO2-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 theGallionellaceae family. One of the Gallionellaceae RubisCOs was purified and shown to possessCO2/O2 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 CO2-fixing enzymes not previously characterized.

Additional publication details

Publication type Article
Publication Subtype Journal Article
Title Functional metagenomic selection of RubisCOs from uncultivated bacteria
Series title Environmental Microbiology
DOI 10.1111/1462-2920.13138
Volume 18
Issue 4
Year Published 2016
Language English
Publisher Wiley
Contributing office(s) National Research Program - Western Branch
Description 13 p.
First page 1187
Last page 1199
Online Only (Y/N) N
Additional Online Files (Y/N) N