Pyrophosphate-Dependent ATP Formation from Acetyl Coenzyme A in Syntrophus aciditrophicus, a New Twist on ATP Formation
Abstract
Syntrophus aciditrophicus is a model syntrophic bacterium that degrades key intermediates in anaerobic decomposition, such as benzoate, cyclohexane-1-carboxylate, and certain fatty acids, to acetate when grown with hydrogen-/formate-consuming microorganisms. ATP formation coupled to acetate production is the main source for energy conservation by S. aciditrophicus. However, the absence of homologs for phosphate acetyltransferase and acetate kinase in the genome of S. aciditrophicus leaves it unclear as to how ATP is formed, as most fermentative bacteria rely on these two enzymes to synthesize ATP from acetyl coenzyme A (CoA) and phosphate. Here, we combine transcriptomic, proteomic, metabolite, and enzymatic approaches to show that S. aciditrophicus uses AMP-forming, acetyl-CoA synthetase (Acs1) for ATP synthesis from acetyl-CoA. acs1 mRNA and Acs1 were abundant in transcriptomes and proteomes, respectively, of S. aciditrophicus grown in pure culture and coculture. Cell extracts of S. aciditrophicus had low or undetectable acetate kinase and phosphate acetyltransferase activities but had high acetyl-CoA synthetase activity under all growth conditions tested. Both Acs1 purified from S. aciditrophicus and recombinantly produced Acs1 catalyzed ATP and acetate formation from acetyl-CoA, AMP, and pyrophosphate. High pyrophosphate levels and a high AMP-to-ATP ratio (5.9 ± 1.4) in S. aciditrophicus cells support the operation of Acs1more »
- Authors:
-
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- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California, USA
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, USA
- Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, California, USA
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California, USA, Department of Biological Chemistry, University of California Los Angeles, Los Angeles, California, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Univ. of Oklahoma, Norman, OK (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences, and Biosciences Division; USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institutes of Health (NIH)
- OSTI Identifier:
- 1784812
- Alternate Identifier(s):
- OSTI ID: 1324038; OSTI ID: 1604787
- Grant/Contract Number:
- FG02-96ER20214; AC05-00OR22725; FC02-02ER63421; R01GM085402; FC02-02ER6342; FG02-08ER64689
- Resource Type:
- Journal Article: Published Article
- Journal Name:
- mBio
- Additional Journal Information:
- Journal Name: mBio Journal Volume: 7 Journal Issue: 4; Journal ID: ISSN 2161-2129
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; syntrophy; bioenergy; methanogenesis
Citation Formats
James, Kimberly L., Ríos-Hernández, Luis A., Wofford, Neil Q., Mouttaki, Housna, Sieber, Jessica R., Sheik, Cody S., Nguyen, Hong H., Yang, Yanan, Xie, Yongming, Erde, Jonathan, Rohlin, Lars, Karr, Elizabeth A., Loo, Joseph A., Ogorzalek Loo, Rachel R., Hurst, Gregory B., Gunsalus, Robert P., Szweda, Luke I., McInerney, Michael J., Harwood, ed., Caroline S., Ferry, J. Greg, Whitman, William, and Kamagata, Yoichi. Pyrophosphate-Dependent ATP Formation from Acetyl Coenzyme A in Syntrophus aciditrophicus, a New Twist on ATP Formation. United States: N. p., 2016.
Web. doi:10.1128/mBio.01208-16.
James, Kimberly L., Ríos-Hernández, Luis A., Wofford, Neil Q., Mouttaki, Housna, Sieber, Jessica R., Sheik, Cody S., Nguyen, Hong H., Yang, Yanan, Xie, Yongming, Erde, Jonathan, Rohlin, Lars, Karr, Elizabeth A., Loo, Joseph A., Ogorzalek Loo, Rachel R., Hurst, Gregory B., Gunsalus, Robert P., Szweda, Luke I., McInerney, Michael J., Harwood, ed., Caroline S., Ferry, J. Greg, Whitman, William, & Kamagata, Yoichi. Pyrophosphate-Dependent ATP Formation from Acetyl Coenzyme A in Syntrophus aciditrophicus, a New Twist on ATP Formation. United States. https://doi.org/10.1128/mBio.01208-16
James, Kimberly L., Ríos-Hernández, Luis A., Wofford, Neil Q., Mouttaki, Housna, Sieber, Jessica R., Sheik, Cody S., Nguyen, Hong H., Yang, Yanan, Xie, Yongming, Erde, Jonathan, Rohlin, Lars, Karr, Elizabeth A., Loo, Joseph A., Ogorzalek Loo, Rachel R., Hurst, Gregory B., Gunsalus, Robert P., Szweda, Luke I., McInerney, Michael J., Harwood, ed., Caroline S., Ferry, J. Greg, Whitman, William, and Kamagata, Yoichi. 2016.
"Pyrophosphate-Dependent ATP Formation from Acetyl Coenzyme A in Syntrophus aciditrophicus, a New Twist on ATP Formation". United States. https://doi.org/10.1128/mBio.01208-16.
@article{osti_1784812,
title = {Pyrophosphate-Dependent ATP Formation from Acetyl Coenzyme A in Syntrophus aciditrophicus, a New Twist on ATP Formation},
author = {James, Kimberly L. and Ríos-Hernández, Luis A. and Wofford, Neil Q. and Mouttaki, Housna and Sieber, Jessica R. and Sheik, Cody S. and Nguyen, Hong H. and Yang, Yanan and Xie, Yongming and Erde, Jonathan and Rohlin, Lars and Karr, Elizabeth A. and Loo, Joseph A. and Ogorzalek Loo, Rachel R. and Hurst, Gregory B. and Gunsalus, Robert P. and Szweda, Luke I. and McInerney, Michael J. and Harwood, ed., Caroline S. and Ferry, J. Greg and Whitman, William and Kamagata, Yoichi},
abstractNote = {Syntrophus aciditrophicus is a model syntrophic bacterium that degrades key intermediates in anaerobic decomposition, such as benzoate, cyclohexane-1-carboxylate, and certain fatty acids, to acetate when grown with hydrogen-/formate-consuming microorganisms. ATP formation coupled to acetate production is the main source for energy conservation by S. aciditrophicus. However, the absence of homologs for phosphate acetyltransferase and acetate kinase in the genome of S. aciditrophicus leaves it unclear as to how ATP is formed, as most fermentative bacteria rely on these two enzymes to synthesize ATP from acetyl coenzyme A (CoA) and phosphate. Here, we combine transcriptomic, proteomic, metabolite, and enzymatic approaches to show that S. aciditrophicus uses AMP-forming, acetyl-CoA synthetase (Acs1) for ATP synthesis from acetyl-CoA. acs1 mRNA and Acs1 were abundant in transcriptomes and proteomes, respectively, of S. aciditrophicus grown in pure culture and coculture. Cell extracts of S. aciditrophicus had low or undetectable acetate kinase and phosphate acetyltransferase activities but had high acetyl-CoA synthetase activity under all growth conditions tested. Both Acs1 purified from S. aciditrophicus and recombinantly produced Acs1 catalyzed ATP and acetate formation from acetyl-CoA, AMP, and pyrophosphate. High pyrophosphate levels and a high AMP-to-ATP ratio (5.9 ± 1.4) in S. aciditrophicus cells support the operation of Acs1 in the acetate-forming direction. Thus, S. aciditrophicus has a unique approach to conserve energy involving pyrophosphate, AMP, acetyl-CoA, and an AMP-forming, acetyl-CoA synthetase.},
doi = {10.1128/mBio.01208-16},
url = {https://www.osti.gov/biblio/1784812},
journal = {mBio},
issn = {2161-2129},
number = 4,
volume = 7,
place = {United States},
year = {Wed Sep 07 00:00:00 EDT 2016},
month = {Wed Sep 07 00:00:00 EDT 2016}
}
Web of Science
Works referenced in this record:
A method for the concentration and for the colorimetric determination of nanomoles of inorganic pyrophosphate
journal, October 1981
- Heinonen, Jukka K.; Honkasalo, Sirpa H.; Kukko, Eila I.
- Analytical Biochemistry, Vol. 117, Issue 1
Benzoate-Coenzyme A Ligase from Thauera aromatica: an Enzyme Acting in Anaerobic and Aerobic Pathways
journal, August 2003
- Schuhle, K.; Gescher, J.; Feil, U.
- Journal of Bacteriology, Vol. 185, Issue 16
Anaerobic microbial metabolism can proceed close to thermodynamic limits
journal, January 2002
- Jackson, Bradley E.; McInerney, Michael J.
- Nature, Vol. 415, Issue 6870
Cyclohexane Carboxylate and Benzoate Formation from Crotonate in Syntrophus aciditrophicus
journal, December 2006
- Mouttaki, H.; Nanny, M. A.; McInerney, M. J.
- Applied and Environmental Microbiology, Vol. 73, Issue 3
The genome of Syntrophus aciditrophicus: Life at the thermodynamic limit of microbial growth
journal, April 2007
- McInerney, M. J.; Rohlin, L.; Mouttaki, H.
- Proceedings of the National Academy of Sciences, Vol. 104, Issue 18
Acetate kinase from Veillonella alcalescens. Regulation of enzyme activity by succinate and substrates.
journal, May 1976
- Bowman, C. M.; Valdez, R. O.; Nishimura, J. S.
- Journal of Biological Chemistry, Vol. 251, Issue 10
Mitochondrial respiration and redox coupling in articular chondrocytes
journal, March 2015
- Lane, Rachel S.; Fu, Yao; Matsuzaki, Satoshi
- Arthritis Research & Therapy, Vol. 17, Issue 1
Genomic Insights into Syntrophy: The Paradigm for Anaerobic Metabolic Cooperation
journal, October 2012
- Sieber, Jessica R.; McInerney, Michael J.; Gunsalus, Robert P.
- Annual Review of Microbiology, Vol. 66, Issue 1
Activation and degradation of benzoate, 3-phenylpropionate and crotonate bySyntrophus buswellii strain GA. Evidence for electron-transport phosphorylation during crotonate respiration
journal, February 1996
- Auburger, G.; Winter, J.
- Applied Microbiology and Biotechnology, Vol. 44, Issue 6
Acetyl Coenzyme A Synthetase (ADP Forming) from the Hyperthermophilic Archaeon Pyrococcus furiosus: Identification, Cloning, Separate Expression of the Encoding Genes,acdAI and acdBI, in Escherichia coli, and In Vitro Reconstitution of the Active Heterotetrameric Enzyme from Its Recombinant Subunits
journal, September 1999
- Musfeldt, Meike; Selig, Martina; Schönheit, Peter
- Journal of Bacteriology, Vol. 181, Issue 18
Energy charge of the adenylate pool as a regulatory parameter. Interaction with feedback modifiers
journal, November 1968
- Atkinson, Daniel E.
- Biochemistry, Vol. 7, Issue 11
Energetics of syntrophic cooperation in methanogenic degradation
journal, June 1997
- Schink, B.
- Microbiology and Molecular Biology Reviews, Vol. 61, Issue 2
P1,P5-Di(Adenosine-5′)Pentaphosphate(Ap5A) as an Inhibitor of Adenylate Kinase in Studies of Fragmented Sarcoplasmic Reticulum from Bullfrog Skeletal Muscle1
journal, July 1980
- Kurebayashi, Nagomi; Kodama, Takao; Ogawa, Yasuo
- The Journal of Biochemistry, Vol. 88, Issue 3
In vivo enzymatic activity of acetylCoA synthetase in skeletal muscle revealed by 13C turnover from hyperpolarized [1-13C]acetate to [1-13C]acetylcarnitine
journal, August 2013
- Bastiaansen, Jessica A. M.; Cheng, Tian; Mishkovsky, Mor
- Biochimica et Biophysica Acta (BBA) - General Subjects, Vol. 1830, Issue 8
Preparation of cell-free extracts and the enzymes involved in fatty acid metabolism in Syntrophomonas wolfei.
journal, July 1986
- Wofford, N. Q.; Beaty, P. S.; McInerney, M. J.
- Journal of Bacteriology, Vol. 167, Issue 1
The Purification and Properties of Phosphotransacetylase
journal, June 1952
- Stadtman, E. R.
- Journal of Biological Chemistry, Vol. 196, Issue 2
The Intracellular Concentration of Pyrophosphate in the Batch Culture of Escherichia coli
journal, October 1982
- Kukko, Eila; Heinonen, Jukka
- European Journal of Biochemistry, Vol. 127, Issue 2
Acetyl-coenzyme A synthetase (AMP forming)
journal, August 2004
- Starai, V. J.; Escalante-Semerena, J. C.
- Cellular and Molecular Life Sciences, Vol. 61, Issue 16
Metabolism of Benzoate, Cyclohex-1-ene Carboxylate, and Cyclohexane Carboxylate by "Syntrophus aciditrophicus" Strain SB in Syntrophic Association with H2-Using Microorganisms
journal, April 2001
- Elshahed, M. S.; Bhupathiraju, V. K.; Wofford, N. Q.
- Applied and Environmental Microbiology, Vol. 67, Issue 4
Syntrophus aciditrophicus sp. nov., a new anaerobic bacterium that degrades fatty acids and benzoate in syntrophic association with hydrogen-using microorganisms
journal, January 1999
- Jackson, Bradley E.; Bhupathiraju, V. K.; Tanner, Ralph S.
- Archives of Microbiology, Vol. 171, Issue 2
Creatine kinase in serum: 1. Determination of optimum reaction conditions.
journal, May 1976
- Szasz, G.; Gruber, W.; Bernt, E.
- Clinical Chemistry, Vol. 22, Issue 5
Syntrophomonas wolfei gen. nov. sp. nov., an Anaerobic, Syntrophic, Fatty Acid-Oxidizing Bacterium
journal, January 1981
- McInerney, M. J.; Bryant, M. P.; Hespell, R. B.
- Applied and Environmental Microbiology, Vol. 41, Issue 4
Purification and characterization of the acetate forming enzyme, acetyl-CoA synthetase (ADP-forming) from the amitochondriate protist, Giardia lamblia
journal, January 1996
- Sanchez, Lidya B.; Müller, Miklós
- FEBS Letters, Vol. 378, Issue 3
Membrane-bound proton-translocating pyrophosphatase of Syntrophus gentianae, a syntrophically benzoate-degrading fermenting bacterium
journal, September 1998
- Schocke, Ludger; Schink, Bernhard
- European Journal of Biochemistry, Vol. 256, Issue 3
Fungal Ammonia Fermentation, a Novel Metabolic Mechanism That Couples the Dissimilatory and Assimilatory Pathways of Both Nitrate and Ethanol: ROLE OF ACETYL CoA SYNTHETASE IN ANAEROBIC ATP SYNTHESIS
journal, January 2004
- Takasaki, Kazuto; Shoun, Hirofumi; Yamaguchi, Masashi
- Journal of Biological Chemistry, Vol. 279, Issue 13
Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
journal, June 2009
- Bennett, Bryson D.; Kimball, Elizabeth H.; Gao, Melissa
- Nature Chemical Biology, Vol. 5, Issue 8
The importance of hydrogen and formate transfer for syntrophic fatty, aromatic and alicyclic metabolism: Importance of interspecies hydrogen and formate transfer
journal, October 2013
- Sieber, Jessica R.; Le, Huynh M.; McInerney, Michael J.
- Environmental Microbiology, Vol. 16, Issue 1
Proteomic analysis reveals metabolic and regulatory systems involved in the syntrophic and axenic lifestyle of Syntrophomonas wolfei
journal, February 2015
- Sieber, Jessica R.; Crable, Bryan R.; Sheik, Cody S.
- Frontiers in Microbiology, Vol. 6