DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: A nitrogenase-like enzyme system catalyzes methionine, ethylene, and methane biogenesis

Journal Article · · Science (Online)
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [4]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [1]
  1. The Ohio State Univ., Columbus, OH (United States)
  2. Colorado State Univ., Fort Collins, CO (United States)
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Chemical Sciences Division
  4. Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Bacterial production of hydrocarbon gases like ethylene and methane affects soil ecosystems and the climate. This study reveals that methane and ethylene from land and freshwater bacteria are directly produced by a previously unknown methionine biosynthesis pathway. This pathway employs a nitrogenase-like reductase that is distinct from known nitrogenases and nitrogenase-like reductases. The nitrogenase-like methylthio-alkane reductase specifically functions in carbon-sulfur bond breakage to reduce ubiquitous and significant volatile organic sulfur compounds such as dimethyl sulfide and (2-methylthio)ethanol. The liberated methanethiol serves as the immediate precursor to methionine. Whereas ethylene or methane is released into the environment. This pathway provides a biological route to the synthesis of ethylene in the absence of oxygen. Finally, anaerobic ethylene production by this pathway apparently explains the long-standing observation of ethylene accumulation in oxygen-depleted soils Methane production reveals an additional bacterial pathway that is distinct from archaeal methanogenesis.

Research Organization:
The Ohio State Univ., Columbus, OH (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER); NCI
Contributing Organization:
University of Colorado Cancer Center’s Genomics and Microarray Core Shared Resource; University of Colorado Boulder Research Computing Group; Environmental Molecular Sciences Laboratory; Battelle and UT-Battelle, LLC
Grant/Contract Number:
SC0019338; AC05-76RLO1830; P30CA046934; AC05-00OR22725
OSTI ID:
1658249
Alternate ID(s):
OSTI ID: 1813253
Journal Information:
Science (Online), Vol. 369, Issue 6507; Related Information: All raw mass spectraand searched data files for the proteome measurements have beendeposited into the ProteomeXchange repository: MassIVE accessionnumber MSV000084455 (FTP link to files: ftp://massive.ucsd.edu/MSV000084455/) and ProteomeXchange accession numberPXD015818. Raw transcriptomics reads are available in the NCBISequence Read Archive under accession numbers SRR10887327through SRR10887338 and BioProject accession number PRJNA601207.; ISSN 1095-9203
Publisher:
AAASCopyright Statement
Country of Publication:
United States
Language:
English

References (58)

Isotopic evidence for biological nitrogen fixation by molybdenum-nitrogenase from 3.2 Gyr journal February 2015
The physiology and habitat of the last universal common ancestor journal July 2016
New insights into the evolutionary history of biological nitrogen fixation journal January 2013
The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea journal October 2016
Elucidation of the biosynthesis of the methane catalyst coenzyme F430 journal February 2017
X-ray crystal structure of the light-independent protochlorophyllide reductase journal May 2010
A Second Nitrogenase-like Enzyme for Bacteriochlorophyll Biosynthesis: RECONSTITUTION OF CHLOROPHYLLIDE a REDUCTASE WITH PURIFIED X-PROTEIN (BchX) AND YZ-PROTEIN (BchY-BchZ) FROM RHODOBACTER CAPSULATUS journal March 2006
Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes journal January 2012
The Natural History of Nitrogen Fixation journal March 2004
Microbial pathway for anaerobic 5′-methylthioadenosine metabolism coupled to ethylene formation journal November 2017
Methylthioadenosine/S-adenosylhomocysteine nucleosidase, a critical enzyme for bacterial metabolism: Involvement of MTA/SAH nucleosidase in bacterial metabolism journal November 2010
Biosynthesis of Nitrogenase Cofactors journal January 2020
Mutagenesis and Functional Characterization of theglnB, glnA, and nifA Genes from the Photosynthetic Bacterium Rhodospirillum rubrum journal February 2000
A RubisCO-like protein links SAM metabolism with isoprenoid biosynthesis journal October 2012
The structure of vanadium nitrogenase reveals an unusual bridging ligand journal July 2017
Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08 Å resolution: comparison with the Azotobacter vinelandii MoFe protein journal January 2015
A bound reaction intermediate sheds light on the mechanism of nitrogenase journal March 2018
Aquatic and terrestrial cyanobacteria produce methane journal January 2020
Marine methane paradox explained by bacterial degradation of dissolved organic matter journal November 2016
A pathway for biological methane production using bacterial iron-only nitrogenase journal January 2018
Occurrence of Ethylene, and its Significance, in Anaerobic Soil journal May 1969
Soil and Crop Management Practices to Minimize the Impact of Waterlogging on Crop Productivity journal February 2019
Identification of Substrates and Isolation of Microorganisms responsible for Ethylene Production in the Soil journal November 1972
Ethylene in soil journal August 1975
A bifunctional salvage pathway for two distinct S‐adenosylmethionine byproducts that is widespread in bacteria, including pathogenic Escherichia coli journal January 2020
Salvage of the 5-deoxyribose byproduct of radical SAM enzymes journal August 2018
E ndomicrobium proavitum , the first isolate of E ndomicrobia class. nov. (phylum E lusimicrobia ) - an ultramicrobacterium with an unusual cell cycle that fixes nitrogen with a Group IV nitrogenase journal July 2015
Mechanistic Diversity in the RuBisCO Superfamily:  The “Enolase” in the Methionine Salvage Pathway in Geobacillus kaustophilus , journal April 2007
Roles of RubisCO and the RubisCO-Like Protein in 5-Methylthioadenosine Metabolism in the Nonsulfur Purple Bacterium Rhodospirillum rubrum journal December 2009
Regulation of Uptake Hydrogenase and Effects of Hydrogen Utilization on Gene Expression in Rhodopseudomonas palustris journal August 2006
Rhodopseudomonas viridis, nov. spec., ein neu isoliertes, obligat phototrophes Bakterium journal January 1966
Light-dependent utilization of organic compounds and photoproduction of molecular hydrogen by photosynthetic bacteria; relationships with nitrogen metabolism journal September 1961
In Vivo Studies in Rhodospirillum rubrum Indicate That Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) Catalyzes Two Obligatorily Required and Physiologically Significant Reactions for Distinct Carbon and Sulfur Metabolic Pathways journal October 2015
Engineered biosynthesis of bacteriochlorophyll b in Rhodobacter sphaeroides journal October 2014
MyriMatch:  Highly Accurate Tandem Mass Spectral Peptide Identification by Multivariate Hypergeometric Analysis journal February 2007
IDPicker 2.0: Improved Protein Assembly with High Discrimination Peptide Identification Filtering journal August 2009
DanteR: an extensible R-based tool for quantitative analysis of -omics data journal July 2012
The Perseus computational platform for comprehensive analysis of (prote)omics data journal June 2016
Fast gapped-read alignment with Bowtie 2 journal March 2012
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 journal December 2014
Genetic analysis of pigment biosynthesis in Xanthobacter autotrophicus Py2 using a new, highly efficient transposon mutagenesis system that is functional in a wide variety of bacteria journal September 2002
Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans journal April 1979
The Acetylene-Ethylene Assay for N 2 Fixation: Laboratory and Field Evaluation journal August 1968
Density‐functional thermochemistry. III. The role of exact exchange journal April 1993
NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations journal September 2010
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability journal January 2013
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses journal June 2009
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies journal November 2014
ModelFinder: fast model selection for accurate phylogenetic estimates journal May 2017
UFBoot2: Improving the Ultrafast Bootstrap Approximation journal October 2017
The EMBL-EBI search and sequence analysis tools APIs in 2019 journal April 2019
Jalview Version 2--a multiple sequence alignment editor and analysis workbench journal January 2009
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database journal November 2019
Electron Transfer to Nitrogenase in Different Genomic and Metabolic Backgrounds journal February 2018
Mechanism of Nitrogen Fixation by Nitrogenase: The Next Stage journal January 2014
Characterization of the DraT/DraG System for Posttranslational Regulation of Nitrogenase in the Endophytic Betaproteobacterium Azoarcus sp. Strain BH72 journal June 2009
ATP-driven Reduction by Dark-operative Protochlorophyllide Oxidoreductase from Chlorobium tepidum Mechanistically Resembles Nitrogenase Catalysis journal February 2008
Catalytic activities of NifEN: Implications for nitrogenase evolution and mechanism journal September 2009