skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Functional metagenomic selection of ribulose 1, 5-bisphosphate carboxylase/oxygenase from uncultivated bacteria

Journal Article · · Environmental Microbiology
 [1];  [1];  [1];  [2];  [3];  [4];  [5];  [6];  [6];  [4];  [1];  [1]
  1. The Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology
  2. Botanical Research Inst. of Texas, Fort Worth,TX (United States)
  3. Univ. of Sao Paulo, Sao Paulo (Brazil). Dept. of Genetics, ESALQ
  4. Univ. of California, Berkeley, CA (United States). Dept. of Earth and Planetary Science
  5. Univ. of California, Los Angeles, CA (United States). Protein Expression Technology Center, UCLA-DOE Inst.
  6. U.S. Geological Survey, Menlo Park, CA (United States)
+ Show Author Affiliations

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 the Gallionellaceae family. One of the Gallionellaceae Rubis COs was purified and shown to possess CO2/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.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)
Grant/Contract Number:
AC02-05CH11231; FC02‐02ER63421
OSTI ID:
1471013
Journal Information:
Environmental Microbiology, Vol. 18, Issue 4; ISSN 1462-2912
Publisher:
WileyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 20 works
Citation information provided by
Web of Science

References (39)

Coupled Arsenotrophy in a Hot Spring Photosynthetic Biofilm at Mono Lake, California journal May 2010
Cloning the Soil Metagenome: a Strategy for Accessing the Genetic and Functional Diversity of Uncultured Microorganisms journal June 2000
Positive and Negative Selection of Mutant Forms of Prokaryotic (Cyanobacterial) Ribulose-1,5-bisphosphate Carboxylase/Oxygenase journal August 2003
A function-based screen for seeking RubisCO active clones from metagenomes: novel enzymes influencing RubisCO activity journal September 2014
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies journal January 2014
Multiple regulators and their interactions in vivo and in vitro with the cbb regulons of Rhodobacter capsulatus11Edited by N.-H. Chua journal July 2000
Role of auxiliary proteins in Rubisco biogenesis and function journal June 2015
CO 2 CONCENTRATING MECHANISMS IN ALGAE: Mechanisms, Environmental Modulation, and Evolution journal June 2005
RubisCO Gene Clusters Found in a Metagenome Microarray from Acid Mine Drainage journal January 2013
A Rubisco Mutant That Confers Growth under a Normally “Inhibitory” Oxygen Concentration journal September 2009
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data journal April 2012
"Green-like" and "Red-like" RubisCO cbbL Genes in Rhodobacter azotoformans journal April 2003
R UBISCO : Structure, Regulatory Interactions, and Possibilities for a Better Enzyme journal June 2002
Unusual biology across a group comprising more than 15% of domain Bacteria journal June 2015
Diversity of Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase Large-Subunit Genes from Groundwater and Aquifer Microorganisms journal June 2003
Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla journal September 2012
Structure-Function Studies with the Unique Hexameric Form II Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) from Rhodopseudomonas palustris journal June 2014
Distribution and phylogenetic diversity of cbbM genes encoding RubisCO form II in a deep-sea hydrothermal field revealed by newly designed PCR primers journal January 2012
Development of an activity-directed selection system enabled significant improvement of the carboxylation efficiency of Rubisco journal May 2014
Phylogenetic and evolutionary relationships of RubisCO and the RubisCO-like proteins and the functional lessons provided by diverse molecular forms journal May 2008
Evolving improved Synechococcus Rubisco functional expression in Escherichia coli journal August 2008
Directed evolution of RuBisCO hypermorphs through genetic selection in engineered E.coli journal January 2006
Bacterioplankton Community Shifts in an Arctic Lake Correlate with Seasonal Changes in Organic Matter Source journal April 2003
Light-dependent utilization of organic compounds and photoproduction of molecular hydrogen by photosynthetic bacteria; relationships with nitrogen metabolism journal September 1961
A faster Rubisco with potential to increase photosynthesis in crops journal September 2014
Arsenic(III) Fuels Anoxygenic Photosynthesis in Hot Spring Biofilms from Mono Lake, California journal August 2008
MUSCLE: multiple sequence alignment with high accuracy and high throughput journal March 2004
Microbial communities in dark oligotrophic volcanic ice cave ecosystems of Mt. Erebus, Antarctica journal March 2015
Synthesis of Catalytically Active Form III Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase in Archaea journal May 2003
Identification of novel esterase-active enzymes from hot environments by use of the host bacterium Thermus thermophilus journal April 2015
Engineering of a Type III Rubisco from a Hyperthermophilic Archaeon in Order To Enhance Catalytic Performance in Mesophilic Host Cells journal August 2007
UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota journal March 2013
Functional Prokaryotic RubisCO from an Oceanic Metagenomic Library journal March 2010
Catalysis and regulation in Rubisco journal June 2007
Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling journal March 2015
DNA recovery from soils of diverse composition. journal January 1996
Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis journal September 2020
Coupled Arsenotrophy in a Hot Spring Photosynthetic Biofilm at Mono Lake, California journal July 2011
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies text January 2014

Cited By (5)

Engineering of a chromogenic enzyme screening system based on an auxiliary indole‐3‐carboxylic acid monooxygenase journal January 2019
Harnessing the power of microbial autotrophy journal September 2016
The evolving interface between synthetic biology and functional metagenomics journal July 2018
A load driver device for engineering modularity in biological networks journal November 2014
Unraveling RubisCO Form I and Form II Regulation in an Uncultured Organism from a Deep-Sea Hydrothermal Vent via Metagenomic and Mutagenesis Studies journal July 2017

Similar Records

Photosynthetic acclimation to elevated CO{sub 2} occurs in transformed tobacco with decreased ribulose-1,5-bisphosphate carboxylase/oxygenase content
Journal Article · Tue Feb 01 00:00:00 EST 1994 · Plant Physiology (Bethesda) · OSTI ID:1471013
Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RubisCO) Is Essential for Growth of the Methanotroph Methylococcus capsulatus Strain Bath
Journal Article · Thu Aug 26 00:00:00 EDT 2021 · Applied and Environmental Microbiology · OSTI ID:1471013
+5 more
Serine 363 of a hydrophobic region of Archaeal ribulose 1,5-bisphosphate carboxylase/oxygenase from Archaeoglobus fulgidus and Thermococcus kodakaraensis affects CO2/O2 substrate specificity and oxygen sensitivity
Journal Article · Fri Sep 18 00:00:00 EDT 2015 · PLoS ONE · OSTI ID:1471013

Related Subjects

59 BASIC BIOLOGICAL SCIENCES