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Title: Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach

Abstract

Biological methane utilization, one of the main sinks of the greenhouse gas in nature, represents an attractive platform for production of fuels and value-added chemicals. Despite the progress made in our understanding of the individual parts of methane utilization, our knowledge of how the whole-cell metabolic network is organized and coordinated is limited. Attractive growth and methane-conversion rates, a complete and expert-annotated genome sequence, as well as large enzymatic, 13C-labeling, and transcriptomic datasets make Methylomicrobium alcaliphilum 20ZR an exceptional model system for investigating methane utilization networks. Here we present a comprehensive metabolic framework of methane and methanol utilization in M. alcaliphilum 20ZR. A set of novel metabolic reactions governing carbon distribution across central pathways in methanotrophic bacteria was predicted by in-silico simulations and confirmed by global non-targeted metabolomics and enzymatic evidences. Our data highlight the importance of substitution of ATP-linked steps with PPi-dependent reactions and support the presence of a carbon shunt from acetyl-CoA to the pentose-phosphate pathway and highly branched TCA cycle. The diverged TCA reactions promote balance between anabolic reactions and redox demands. As a result, the computational framework of C1-metabolism in methanotrophic bacteria can represent an efficient tool for metabolic engineering or ecosystem modeling.

Authors:
 [1];  [2];  [2];  [3];  [3];  [4]; ORCiD logo [4];  [2]
  1. San Diego State Univ., San Diego, CA (United States); Institute of Cytology and Genetics and Novosibirsk State Univ., Novosibirsk (Russia)
  2. San Diego State Univ., San Diego, CA (United States)
  3. Metabolon, Inc., Durham, NC (United States)
  4. National Renewable Energy Lab. (NREL), Golden, CO (United States)
Publication Date:
Research Org.:
National Renewable Energy Lab. (NREL), Golden, CO (United States)
Sponsoring Org.:
USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office
OSTI Identifier:
1422031
Report Number(s):
NREL/JA-5100-70511
Journal ID: ISSN 2045-2322
Grant/Contract Number:  
AC36-08GO28308
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; metabolic engineering; methane utilization; methylomicrobium alcaliphilum

Citation Formats

Akberdin, Ilya R., Thompson, Merlin, Hamilton, Richard, Desai, Nalini, Alexander, Danny, Henard, Calvin A., Guarnieri, Michael T., and Kalyuzhnaya, Marina G. Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach. United States: N. p., 2018. Web. doi:10.1038/s41598-018-20574-z.
Akberdin, Ilya R., Thompson, Merlin, Hamilton, Richard, Desai, Nalini, Alexander, Danny, Henard, Calvin A., Guarnieri, Michael T., & Kalyuzhnaya, Marina G. Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach. United States. doi:10.1038/s41598-018-20574-z.
Akberdin, Ilya R., Thompson, Merlin, Hamilton, Richard, Desai, Nalini, Alexander, Danny, Henard, Calvin A., Guarnieri, Michael T., and Kalyuzhnaya, Marina G. Tue . "Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach". United States. doi:10.1038/s41598-018-20574-z. https://www.osti.gov/servlets/purl/1422031.
@article{osti_1422031,
title = {Methane utilization in Methylomicrobium alcaliphilum 20ZR: a systems approach},
author = {Akberdin, Ilya R. and Thompson, Merlin and Hamilton, Richard and Desai, Nalini and Alexander, Danny and Henard, Calvin A. and Guarnieri, Michael T. and Kalyuzhnaya, Marina G.},
abstractNote = {Biological methane utilization, one of the main sinks of the greenhouse gas in nature, represents an attractive platform for production of fuels and value-added chemicals. Despite the progress made in our understanding of the individual parts of methane utilization, our knowledge of how the whole-cell metabolic network is organized and coordinated is limited. Attractive growth and methane-conversion rates, a complete and expert-annotated genome sequence, as well as large enzymatic, 13C-labeling, and transcriptomic datasets make Methylomicrobium alcaliphilum 20ZR an exceptional model system for investigating methane utilization networks. Here we present a comprehensive metabolic framework of methane and methanol utilization in M. alcaliphilum 20ZR. A set of novel metabolic reactions governing carbon distribution across central pathways in methanotrophic bacteria was predicted by in-silico simulations and confirmed by global non-targeted metabolomics and enzymatic evidences. Our data highlight the importance of substitution of ATP-linked steps with PPi-dependent reactions and support the presence of a carbon shunt from acetyl-CoA to the pentose-phosphate pathway and highly branched TCA cycle. The diverged TCA reactions promote balance between anabolic reactions and redox demands. As a result, the computational framework of C1-metabolism in methanotrophic bacteria can represent an efficient tool for metabolic engineering or ecosystem modeling.},
doi = {10.1038/s41598-018-20574-z},
journal = {Scientific Reports},
number = 1,
volume = 8,
place = {United States},
year = {2018},
month = {2}
}

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Cited by: 12 works
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Works referenced in this record:

A methanotroph-based biorefinery: Potential scenarios for generating multiple products from a single fermentation
journal, September 2016


Methanotrophs and copper
journal, July 2010


Production of vitamin B12 in aerobic methylotrophic bacteria
journal, July 2006


BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
journal, October 2015

  • King, Zachary A.; Lu, Justin; Dräger, Andreas
  • Nucleic Acids Research, Vol. 44, Issue D1
  • DOI: 10.1093/nar/gkv1049

Classification of halo(alkali)philic and halo(alkali)tolerant methanotrophs provisionally assigned to the genera Methylomicrobium and Methylobacter and emended description of the genus Methylomicrobium
journal, March 2008

  • Kalyuzhnaya, M. G.; Khmelenina, V.; Eshinimaev, B.
  • INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 58, Issue 3
  • DOI: 10.1099/ijs.0.65317-0

The γ-aminobutyric acid shunt contributes to closing the tricarboxylic acid cycle in S ynechocystis sp. PCC 6803 : The γ-aminobutyric acid shunt in
journal, July 2014

  • Xiong, Wei; Brune, Daniel; Vermaas, Wim F. J.
  • Molecular Microbiology, Vol. 93, Issue 4
  • DOI: 10.1111/mmi.12699

Growth yields of methanotrophs: 1. Effect of copper on the energetics of methane oxidation
journal, March 1986

  • Leak, David J.; Dalton, Howard
  • Applied Microbiology and Biotechnology, Vol. 23, Issue 6
  • DOI: 10.1007/BF02346062

Simultaneously Mitigating Near-Term Climate Change and Improving Human Health and Food Security
journal, January 2012


Whole-genome sequencing identifies common-to-rare variants associated with human blood metabolites
journal, March 2017

  • Long, Tao; Hicks, Michael; Yu, Hung-Chun
  • Nature Genetics, Vol. 49, Issue 4
  • DOI: 10.1038/ng.3809

The properties and potential metabolic role of glucokinase in halotolerant obligate methanotroph Methylomicrobium alcaliphilum 20Z
journal, December 2016

  • Mustakhimov, Ildar I.; Rozova, Olga N.; Solntseva, Natalia P.
  • Antonie van Leeuwenhoek, Vol. 110, Issue 3
  • DOI: 10.1007/s10482-016-0809-z

A 21st-century shift from fossil-fuel to biogenic methane emissions indicated by 13CH4
journal, March 2016


Bioconversion of methane to lactate by an obligate methanotrophic bacterium
journal, February 2016

  • Henard, Calvin A.; Smith, Holly; Dowe, Nancy
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep21585

Modularity of methylotrophy, revisited: Modularity of methylotrophy, revisited
journal, March 2011


Phosphoketolase overexpression increases biomass and lipid yield from methane in an obligate methanotrophic biocatalyst
journal, May 2017


Oxygen-limited metabolism in the methanotroph Methylomicrobium buryatense 5GB1C
journal, January 2017


A distinct pathway for tetrahymanol synthesis in bacteria
journal, October 2015

  • Banta, Amy B.; Wei, Jeremy H.; Welander, Paula V.
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 44
  • DOI: 10.1073/pnas.1511482112

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
journal, August 2011

  • Schellenberger, Jan; Que, Richard; Fleming, Ronan M. T.
  • Nature Protocols, Vol. 6, Issue 9
  • DOI: 10.1038/nprot.2011.308

Genome Sequence of the Haloalkaliphilic Methanotrophic Bacterium Methylomicrobium alcaliphilum 20Z
journal, December 2011

  • Vuilleumier, S.; Khmelenina, V. N.; Bringel, F.
  • Journal of Bacteriology, Vol. 194, Issue 2
  • DOI: 10.1128/JB.06392-11

Arabinose is metabolized via a phosphoketolase pathway in Clostridium acetobutylicum ATCC 824
journal, August 2012

  • Servinsky, M. D.; Germane, K. L.; Liu, S.
  • Journal of Industrial Microbiology & Biotechnology, Vol. 39, Issue 12
  • DOI: 10.1007/s10295-012-1186-x

Properties of recombinant ATP-dependent fructokinase from the halotolerant methanotroph Methylomicrobium alcaliphilum 20Z
journal, April 2012


Highly efficient methane biocatalysis revealed in a methanotrophic bacterium
journal, December 2013

  • Kalyuzhnaya, M. G.; Yang, S.; Rozova, O. N.
  • Nature Communications, Vol. 4, Issue 1
  • DOI: 10.1038/ncomms3785

Constraint-based models predict metabolic and associated cellular functions
journal, January 2014

  • Bordbar, Aarash; Monk, Jonathan M.; King, Zachary A.
  • Nature Reviews Genetics, Vol. 15, Issue 2
  • DOI: 10.1038/nrg3643

The Expanding World of Methylotrophic Metabolism
journal, October 2009


Modeling methanogenesis with a genome‐scale metabolic reconstruction of Methanosarcina barkeri
journal, January 2006

  • Feist, Adam M.; Scholten, Johannes C. M.; Palsson, Bernhard Ø
  • Molecular Systems Biology, Vol. 2, Issue 1
  • DOI: 10.1038/msb4100046

PQQ-dependent methanol dehydrogenases: rare-earth elements make a difference
journal, May 2014

  • Keltjens, Jan T.; Pol, Arjan; Reimann, Joachim
  • Applied Microbiology and Biotechnology, Vol. 98, Issue 14
  • DOI: 10.1007/s00253-014-5766-8

Unusual cyanobacterial TCA cycles: not broken just different
journal, September 2012


Allosteric Regulation of Lactobacillus plantarum Xylulose 5-Phosphate/Fructose 6-Phosphate Phosphoketolase (Xfp)
journal, January 2015

  • Glenn, Katie; Smith, Kerry S.
  • Journal of Bacteriology, Vol. 197, Issue 7
  • DOI: 10.1128/JB.02380-14

Isolation and Characterization of Halotolerant Alkaliphilic Methanotrophic Bacteria from Tuva Soda Lakes
journal, November 1997


Characterization of the ectoine biosynthesis genes of haloalkalotolerant obligate methanotroph “Methylomicrobium alcaliphilum 20Z”
journal, November 2005

  • Reshetnikov, Alexander S.; Khmelenina, Valentina N.; Trotsenko, Yuri A.
  • Archives of Microbiology, Vol. 184, Issue 5
  • DOI: 10.1007/s00203-005-0042-z

Envisioning the Bioconversion of Methane to Liquid Fuels
journal, February 2014


Rethinking biological activation of methane and conversion to liquid fuels
journal, April 2014


Methane as a Resource: Can the Methanotrophs Add Value?
journal, March 2015

  • Strong, P. J.; Xie, S.; Clarke, W. P.
  • Environmental Science & Technology, Vol. 49, Issue 7
  • DOI: 10.1021/es504242n

Acetate kinase-an enzyme of the postulated phosphoketolase pathway in Methylomicrobium alcaliphilum 20Z
journal, August 2015

  • Rozova, Olga N.; Khmelenina, Valentina N.; Gavletdinova, Juliya Z.
  • Antonie van Leeuwenhoek, Vol. 108, Issue 4
  • DOI: 10.1007/s10482-015-0549-5

A new method for rapid determination of carbohydrate and total carbon concentrations using UV spectrophotometry
journal, September 2013


Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1
journal, January 2011

  • Peyraud, Rémi; Schneider, Kathrin; Kiefer, Patrick
  • BMC Systems Biology, Vol. 5, Issue 1
  • DOI: 10.1186/1752-0509-5-189

Characterization of recombinant pyrophosphate-dependent 6-phosphofructokinase from halotolerant methanotroph Methylomicrobium alcaliphilum 20Z
journal, December 2010

  • Rozova, Olga N.; Khmelenina, Valentina N.; Vuilleumier, Stéphane
  • Research in Microbiology, Vol. 161, Issue 10
  • DOI: 10.1016/j.resmic.2010.09.009

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
journal, August 2015


Genomic Insights into Methanotrophy: The Complete Genome Sequence of Methylococcus capsulatus (Bath)
journal, September 2004


From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model
journal, June 2016

  • Cuevas, Daniel A.; Edirisinghe, Janaka; Henry, Chris S.
  • Frontiers in Microbiology, Vol. 7
  • DOI: 10.3389/fmicb.2016.00907

Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1)
journal, November 2015

  • de la Torre, Andrea; Metivier, Aisha; Chu, Frances
  • Microbial Cell Factories, Vol. 14, Issue 1
  • DOI: 10.1186/s12934-015-0377-3

Sucrose metabolism in halotolerant methanotroph Methylomicrobium alcaliphilum 20Z
journal, January 2015

  • But, Sergey Y.; Khmelenina, Valentina N.; Reshetnikov, Alexander S.
  • Archives of Microbiology, Vol. 197, Issue 3
  • DOI: 10.1007/s00203-015-1080-9

Biochemical properties and phylogeny of hydroxypyruvate reductases from methanotrophic bacteria with different c1-assimilation pathways
journal, November 2017


Structure of an integral membrane sterol reductase from Methylomicrobium alcaliphilum
journal, October 2014

  • Li, Xiaochun; Roberti, Rita; Blobel, Günter
  • Nature, Vol. 517, Issue 7532
  • DOI: 10.1038/nature13797

Reversing methanogenesis to capture methane for liquid biofuel precursors
journal, January 2016

  • Soo, Valerie W. C.; McAnulty, Michael J.; Tripathi, Arti
  • Microbial Cell Factories, Vol. 15, Issue 1
  • DOI: 10.1186/s12934-015-0397-z

Osmoadaptation in halophilic and alkaliphilic methanotrophs
journal, October 1999

  • Khmelenina, Valentina N.; Kalyuzhnaya, Marina G.; Sakharovsky, Valentin G.
  • Archives of Microbiology, Vol. 172, Issue 5
  • DOI: 10.1007/s002030050786

Highly sensitive determination of ectoine and other compatible solutes by anion-exchange chromatography and pulsed amperometric detection
journal, September 2003

  • Riis, Volker; Maskow, Thomas; Babel, Wolfgang
  • Analytical and Bioanalytical Chemistry, Vol. 377, Issue 1
  • DOI: 10.1007/s00216-003-2085-9

What is flux balance analysis?
journal, March 2010

  • Orth, Jeffrey D.; Thiele, Ines; Palsson, Bernhard Ø
  • Nature Biotechnology, Vol. 28, Issue 3
  • DOI: 10.1038/nbt.1614

Characterization of two recombinant 3-hexulose-6-phosphate synthases from the halotolerant obligate methanotroph Methylomicrobium alcaliphilum 20Z
journal, February 2017


Fatty Acid Biosynthesis Pathways in Methylomicrobium buryatense 5G(B1)
journal, January 2017

  • Demidenko, Aleksandr; Akberdin, Ilya R.; Allemann, Marco
  • Frontiers in Microbiology, Vol. 7
  • DOI: 10.3389/fmicb.2016.02167

Role of NAD+-Dependent Malate Dehydrogenase in the Metabolism of Methylomicrobium alcaliphilum 20Z and Methylosinus trichosporium OB3b
journal, February 2015


Aerobic and anaerobic starvation metabolism in methanotrophic bacteria.
journal, January 1995


Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.
journal, January 1994


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    • DOI: 10.1039/c9gc03722e

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    Metabolic role of pyrophosphate-linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z
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    Rare Earth Elements Alter Redox Balance in Methylomicrobium alcaliphilum 20ZR
    journal, November 2018

    • Akberdin, Ilya R.; Collins, David A.; Hamilton, Richard
    • Frontiers in Microbiology, Vol. 9
    • DOI: 10.3389/fmicb.2018.02735

    Native top-down mass spectrometry provides insights into the copper centers of membrane-bound methane monooxygenase
    journal, June 2019


    Reconstruction of a Genome Scale Metabolic Model of the polyhydroxybutyrate producing methanotroph Methylocystis parvus OBBP
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