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Title: Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria

Abstract

Copper-containing membrane monooxygenases (CuMMOs) are encoded by xmoCAB(D) gene clusters and catalyze the oxidation of methane, ammonia, or some short-chain alkanes and alkenes. In a metagenome constructed from an oilsands tailings pond we detected an xmoCABD gene cluster with <59% derived protein sequence identity to genes from known bacteria. Stable isotope probing experiments combined with a specific xmoA qPCR assay demonstrated that the bacteria possessing these genes were incapable of methane assimilation, but did grow on ethane and propane. Single-cell amplified genomes (SAGs) from propane-enriched samples were screened with the specific PCR assay to identify bacteria possessing the target gene cluster. Multiple SAGs of Betaproteobacteria belonging to the genera Rhodoferax and Polaromonas possessed homologues of the metagenomic xmoCABD gene cluster. Unexpectedly, each of these two genera also possessed other xmoCABD paralogs, representing two additional lineages in phylogenetic analyses. Metabolic reconstructions from SAGs predicted that neither bacterium encoded enzymes with the potential to support catabolic methane or ammonia oxidation, but that both were capable of higher n-alkane degradation. The involvement of the encoded CuMMOs in alkane oxidation was further suggested by reverse transcription PCR analyses, which detected elevated transcription of the xmoA genes upon enrichment of water samples with propane asmore » the sole energy source. Enrichments, isotope incorporation studies, genome reconstructions, and gene expression studies therefore all agreed that the unknown xmoCABD operons did not encode methane or ammonia monooxygenases, but rather n-alkane monooxygenases. Finally, this study broadens the known diversity of CuMMOs and identifies these enzymes in non-nitrifying Betaproteobacteria.« less

Authors:
 [1];  [2];  [1];  [3]; ORCiD logo [4];  [1];  [1];  [5];  [2]; ORCiD logo [5]; ORCiD logo [1]; ORCiD logo [1]
  1. Univ. of Calgary, AB (Canada)
  2. Korea Inst. of Science and Technology, Daejeon (Korea)
  3. Univ. of Calgary, AB (Canada); Univ. of Novi Sad (Serbia)
  4. Univ. of Calgary, AB (Canada); Inst. Tecnologico y de Estudios Superiores de Monterrey, Chihuahua (Mexico)
  5. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); Natural Sciences and Engineering Research Council of Canada (NSERC); National Research Foundation of Korea (NRF)
OSTI Identifier:
1597723
Grant/Contract Number:  
AC02-05CH11231; CRDPJ478071–14; 2014-05067; 2018K1A3A1A74065626
Resource Type:
Accepted Manuscript
Journal Name:
The ISME Journal
Additional Journal Information:
Journal Volume: 14; Journal Issue: 3; Journal ID: ISSN 1751-7362
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; metagenomics; microbial ecology; water microbiology

Citation Formats

Rochman, Fauziah F., Kwon, Miye, Khadka, Roshan, Tamas, Ivica, Lopez-Jauregui, Azriel Abraham, Sheremet, Andriy, V. Smirnova, Angela, Malmstrom, Rex R., Yoon, Sukhwan, Woyke, Tanja, Dunfield, Peter F., and Verbeke, Tobin J. Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria. United States: N. p., 2019. Web. doi:10.1038/s41396-019-0561-2.
Rochman, Fauziah F., Kwon, Miye, Khadka, Roshan, Tamas, Ivica, Lopez-Jauregui, Azriel Abraham, Sheremet, Andriy, V. Smirnova, Angela, Malmstrom, Rex R., Yoon, Sukhwan, Woyke, Tanja, Dunfield, Peter F., & Verbeke, Tobin J. Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria. United States. doi:10.1038/s41396-019-0561-2.
Rochman, Fauziah F., Kwon, Miye, Khadka, Roshan, Tamas, Ivica, Lopez-Jauregui, Azriel Abraham, Sheremet, Andriy, V. Smirnova, Angela, Malmstrom, Rex R., Yoon, Sukhwan, Woyke, Tanja, Dunfield, Peter F., and Verbeke, Tobin J. Tue . "Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria". United States. doi:10.1038/s41396-019-0561-2.
@article{osti_1597723,
title = {Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane-utilizing Betaproteobacteria},
author = {Rochman, Fauziah F. and Kwon, Miye and Khadka, Roshan and Tamas, Ivica and Lopez-Jauregui, Azriel Abraham and Sheremet, Andriy and V. Smirnova, Angela and Malmstrom, Rex R. and Yoon, Sukhwan and Woyke, Tanja and Dunfield, Peter F. and Verbeke, Tobin J.},
abstractNote = {Copper-containing membrane monooxygenases (CuMMOs) are encoded by xmoCAB(D) gene clusters and catalyze the oxidation of methane, ammonia, or some short-chain alkanes and alkenes. In a metagenome constructed from an oilsands tailings pond we detected an xmoCABD gene cluster with <59% derived protein sequence identity to genes from known bacteria. Stable isotope probing experiments combined with a specific xmoA qPCR assay demonstrated that the bacteria possessing these genes were incapable of methane assimilation, but did grow on ethane and propane. Single-cell amplified genomes (SAGs) from propane-enriched samples were screened with the specific PCR assay to identify bacteria possessing the target gene cluster. Multiple SAGs of Betaproteobacteria belonging to the genera Rhodoferax and Polaromonas possessed homologues of the metagenomic xmoCABD gene cluster. Unexpectedly, each of these two genera also possessed other xmoCABD paralogs, representing two additional lineages in phylogenetic analyses. Metabolic reconstructions from SAGs predicted that neither bacterium encoded enzymes with the potential to support catabolic methane or ammonia oxidation, but that both were capable of higher n-alkane degradation. The involvement of the encoded CuMMOs in alkane oxidation was further suggested by reverse transcription PCR analyses, which detected elevated transcription of the xmoA genes upon enrichment of water samples with propane as the sole energy source. Enrichments, isotope incorporation studies, genome reconstructions, and gene expression studies therefore all agreed that the unknown xmoCABD operons did not encode methane or ammonia monooxygenases, but rather n-alkane monooxygenases. Finally, this study broadens the known diversity of CuMMOs and identifies these enzymes in non-nitrifying Betaproteobacteria.},
doi = {10.1038/s41396-019-0561-2},
journal = {The ISME Journal},
number = 3,
volume = 14,
place = {United States},
year = {2019},
month = {12}
}

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