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

Title: Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea

Abstract

Methyl-coenzyme M reductase (MCR), found in strictly anaerobic methanogenic and methanotrophic archaea, catalyzes the reversible production and consumption of the potent greenhouse gas methane. The α subunit of MCR (McrA) contains several unusual post-translational modifications, including a rare thioamidation of glycine. Based on the presumed function of homologous genes involved in the biosynthesis of thioviridamide, a thioamide-containing natural product, we hypothesized that the archaeal tfuA and ycaO genes would be responsible for post-translational installation of thioglycine into McrA. Mass spectrometric characterization of McrA from the methanogenic archaeon Methanosarcina acetivorans lacking tfuA and/or ycaO revealed the presence of glycine, rather than thioglycine, supporting this hypothesis. Phenotypic characterization of the ΔycaO-tfuA mutant revealed a severe growth rate defect on substrates with low free energy yields and at elevated temperatures (39°C - 45°C). Thus, our analyses support a role for thioglycine in stabilizing the protein secondary structure near the active site.

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [4]
  1. Univ. of Illinois at Urbana-Champaign, IL (United States). Carl R. Woese Inst. for Genomic Biology
  2. Univ. of Illinois at Urbana-Champaign, IL (United States). Dept. of Chemistry
  3. Univ. of Illinois at Urbana-Champaign, IL (United States). Carl R. Woese Inst. for Genomic Biology and Dept. of Chemistry and Dept. of Microbiology
  4. Univ. of Illinois at Urbana-Champaign, IL (United States). Carl R. Woese Inst. for Genomic Biology and Dept. of Microbiology
Publication Date:
Research Org.:
Univ. of Illinois at Urbana-Champaign, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Chemical Sciences, Geosciences & Biosciences Division; National Institutes of Health (NIH); Simons Foundation; Life Sciences Research Foundation (LSRF)
OSTI Identifier:
1378144
Alternate Identifier(s):
OSTI ID: 1378147; OSTI ID: 1429098; OSTI ID: 1595337
Grant/Contract Number:  
FG02-02ER15296; GM097142
Resource Type:
Published Article
Journal Name:
eLife
Additional Journal Information:
Journal Name: eLife Journal Volume: 6; Journal ID: ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; 03 NATURAL GAS

Citation Formats

Nayak, Dipti D., Mahanta, Nilkamal, Mitchell, Douglas A., and Metcalf, William W. Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea. United States: N. p., 2017. Web. doi:10.7554/eLife.29218.
Nayak, Dipti D., Mahanta, Nilkamal, Mitchell, Douglas A., & Metcalf, William W. Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea. United States. doi:10.7554/eLife.29218.
Nayak, Dipti D., Mahanta, Nilkamal, Mitchell, Douglas A., and Metcalf, William W. Thu . "Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea". United States. doi:10.7554/eLife.29218.
@article{osti_1378144,
title = {Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic Archaea},
author = {Nayak, Dipti D. and Mahanta, Nilkamal and Mitchell, Douglas A. and Metcalf, William W.},
abstractNote = {Methyl-coenzyme M reductase (MCR), found in strictly anaerobic methanogenic and methanotrophic archaea, catalyzes the reversible production and consumption of the potent greenhouse gas methane. The α subunit of MCR (McrA) contains several unusual post-translational modifications, including a rare thioamidation of glycine. Based on the presumed function of homologous genes involved in the biosynthesis of thioviridamide, a thioamide-containing natural product, we hypothesized that the archaeal tfuA and ycaO genes would be responsible for post-translational installation of thioglycine into McrA. Mass spectrometric characterization of McrA from the methanogenic archaeon Methanosarcina acetivorans lacking tfuA and/or ycaO revealed the presence of glycine, rather than thioglycine, supporting this hypothesis. Phenotypic characterization of the ΔycaO-tfuA mutant revealed a severe growth rate defect on substrates with low free energy yields and at elevated temperatures (39°C - 45°C). Thus, our analyses support a role for thioglycine in stabilizing the protein secondary structure near the active site.},
doi = {10.7554/eLife.29218},
journal = {eLife},
number = ,
volume = 6,
place = {United States},
year = {2017},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.7554/eLife.29218

Citation Metrics:
Cited by: 22 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Biosynthesis of the Antimetabolite 6-Thioguanine in Erwinia amylovora Plays a Key Role in Fire Blight Pathogenesis
journal, August 2013

  • Coyne, Sébastien; Chizzali, Cornelia; Khalil, Mohammed N. A.
  • Angewandte Chemie International Edition, Vol. 52, Issue 40
  • DOI: 10.1002/anie.201305595

YcaO domains use ATP to activate amide backbones during peptide cyclodehydrations
journal, April 2012

  • Dunbar, Kyle L.; Melby, Joel O.; Mitchell, Douglas A.
  • Nature Chemical Biology, Vol. 8, Issue 6
  • DOI: 10.1038/nchembio.944

The Biosynthesis of Methylated Amino Acids in the Active Site Region of Methyl-coenzyme M Reductase
journal, February 2000

  • Selmer, Thorsten; Kahnt, Jörg; Goubeaud, Marcel
  • Journal of Biological Chemistry, Vol. 275, Issue 6
  • DOI: 10.1074/jbc.275.6.3755

Cloning and Heterologous Expression of the Thioviridamide Biosynthesis Gene Cluster from Streptomyces olivoviridis
journal, August 2013

  • Izawa, Masumi; Kawasaki, Takashi; Hayakawa, Yoichi
  • Applied and Environmental Microbiology, Vol. 79, Issue 22
  • DOI: 10.1128/AEM.01978-13

The Genome of M. acetivorans Reveals Extensive Metabolic and Physiological Diversity
journal, April 2002


Sch 18640. A new thiostrepton-type antibiotic
journal, August 1981

  • Puar, M. S.; Ganguly, A. K.; Afonso, A.
  • Journal of the American Chemical Society, Vol. 103, Issue 17
  • DOI: 10.1021/ja00407a047

Two genetically distinct methyl-coenzyme M reductases in Methanobacterium thermoautotrophicum strain Marburg and DeltaH
journal, December 1990


Bacterial gene import and mesophilic adaptation in archaea
journal, June 2015

  • López-García, Purificación; Zivanovic, Yvan; Deschamps, Philippe
  • Nature Reviews Microbiology, Vol. 13, Issue 7
  • DOI: 10.1038/nrmicro3485

Genetic Analysis of the Methanol- and Methylamine-Specific Methyltransferase 2 Genes of Methanosarcina acetivorans C2A
journal, March 2008

  • Bose, A.; Pritchett, M. A.; Metcalf, W. W.
  • Journal of Bacteriology, Vol. 190, Issue 11
  • DOI: 10.1128/JB.00117-08

A Methanogenic Archaeon from Ace Lake, Antarctica: Methanococcoides burtonii sp. nov.
journal, December 1992


Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis
journal, August 2014

  • Dunbar, Kyle L.; Chekan, Jonathan R.; Cox, Courtney L.
  • Nature Chemical Biology, Vol. 10, Issue 10
  • DOI: 10.1038/nchembio.1608

Elucidation of the biosynthesis of the methane catalyst coenzyme F430
journal, February 2017

  • Moore, Simon J.; Sowa, Sven T.; Schuchardt, Christopher
  • Nature, Vol. 543, Issue 7643
  • DOI: 10.1038/nature21427

Evidence That ThiI, an Enzyme Shared between Thiamin and 4-Thiouridine Biosynthesis, May Be a Sulfurtransferase That Proceeds through a Persulfide Intermediate
journal, March 2000

  • Palenchar, Peter M.; Buck, Christopher J.; Cheng, Hui
  • Journal of Biological Chemistry, Vol. 275, Issue 12
  • DOI: 10.1074/jbc.275.12.8283

Comparison of three methyl-coenzyme M reductases from phylogenetically distant organisms: unusual amino acid modification, conservation and adaptation
journal, October 2000

  • Grabarse, Wolfgang; Mahlert, Felix; Shima, Seigo
  • Journal of Molecular Biology, Vol. 303, Issue 2
  • DOI: 10.1006/jmbi.2000.4136

IscS Functions as a Primary Sulfur-donating Enzyme by Interacting Specifically with MoeB and MoaD in the Biosynthesis of Molybdopterin in Escherichia coli
journal, November 2009

  • Zhang, Wanjiao; Urban, Alexander; Mihara, Hisaaki
  • Journal of Biological Chemistry, Vol. 285, Issue 4
  • DOI: 10.1074/jbc.M109.082172

Genome mining for methanobactins
journal, February 2013


Methanobactin, a Copper-Acquisition Compound from Methane-Oxidizing Bacteria
journal, September 2004


Molybdenum Cofactor Biosynthesis in Humans:  Identification of a Persulfide Group in the Rhodanese-like Domain of MOCS3 by Mass Spectrometry
journal, May 2005

  • Matthies, Andreas; Nimtz, Manfred; Leimkühler, Silke
  • Biochemistry, Vol. 44, Issue 21
  • DOI: 10.1021/bi0503448

Ubiquitin-like protein activation by E1 enzymes: the apex for downstream signalling pathways
journal, April 2009

  • Schulman, Brenda A.; Wade Harper, J.
  • Nature Reviews Molecular Cell Biology, Vol. 10, Issue 5
  • DOI: 10.1038/nrm2673

Identification of an Auxiliary Leader Peptide-Binding Protein Required for Azoline Formation in Ribosomal Natural Products
journal, June 2015

  • Dunbar, Kyle L.; Tietz, Jonathan I.; Cox, Courtney L.
  • Journal of the American Chemical Society, Vol. 137, Issue 24
  • DOI: 10.1021/jacs.5b04682

The radical mechanism of biological methane synthesis by methyl-coenzyme M reductase
journal, May 2016


Purified Methyl-Coenzyme-M Reductase is Activated when the Enzyme-Bound Coenzyme F430 is Reduced to the Nickel(I) Oxidation State by Titanium(III) Citrate
journal, January 1997


Different Biosynthetic Pathways to Fosfomycin in Pseudomonas syringae and Streptomyces Species
journal, May 2012

  • Kim, Seung Young; Ju, Kou-San; Metcalf, William W.
  • Antimicrobial Agents and Chemotherapy, Vol. 56, Issue 8
  • DOI: 10.1128/AAC.06478-11

On the mechanism of biological methane formation: structural evidence for conformational changes in methyl-coenzyme M reductase upon substrate binding
journal, May 2001

  • Grabarse, Wolfgang; Mahlert, Felix; Duin, Evert C.
  • Journal of Molecular Biology, Vol. 309, Issue 1
  • DOI: 10.1006/jmbi.2001.4647

Protein splicing and autoproteolysis mechanisms
journal, October 1997


Chemistry and Biology of the Copper Chelator Methanobactin
journal, November 2011

  • Kenney, Grace E.; Rosenzweig, Amy C.
  • ACS Chemical Biology, Vol. 7, Issue 2
  • DOI: 10.1021/cb2003913

Structure of Thioviridamide, a Novel Apoptosis Inducer from Streptomyces olivoviridis
journal, January 2006

  • Hayakawa, Yoichi; Sasaki, Kahori; Nagai, Koji
  • The Journal of Antibiotics, Vol. 59, Issue 1
  • DOI: 10.1038/ja.2006.2

Hydrogen Bonding Abilities of Thioamide
journal, August 2002

  • Lee, Ho-Jin; Choi, Young-Sang; Lee, Kang-Bong
  • The Journal of Physical Chemistry A, Vol. 106, Issue 30
  • DOI: 10.1021/jp025516e

The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea
journal, October 2016


A prevalent peptide-binding domain guides ribosomal natural product biosynthesis
journal, July 2015

  • Burkhart, Brandon J.; Hudson, Graham A.; Dunbar, Kyle L.
  • Nature Chemical Biology, Vol. 11, Issue 8
  • DOI: 10.1038/nchembio.1856

Closthioamide: An Unprecedented Polythioamide Antibiotic from the Strictly Anaerobic Bacterium Clostridium cellulolyticum
journal, February 2010

  • Lincke, Thorger; Behnken, Swantje; Ishida, Keishi
  • Angewandte Chemie, Vol. 122, Issue 11
  • DOI: 10.1002/ange.200906114

In-gel digestion for mass spectrometric characterization of proteins and proteomes
journal, December 2006


Novel reactions involved in energy conservation by methanogenic archaea
journal, September 1999


A genetic system for Archaea of the genus Methanosarcina: Liposome-mediated transformation and construction of shuttle vectors
journal, March 1997

  • Metcalf, W. W.; Zhang, J. K.; Apolinario, E.
  • Proceedings of the National Academy of Sciences, Vol. 94, Issue 6
  • DOI: 10.1073/pnas.94.6.2626

Nonprotein amino acids from Cycas revoluta
journal, June 1997


Total structure of the highly modified peptide antibiotic components of thiopeptin.
journal, January 1983


The physiology and habitat of the last universal common ancestor
journal, July 2016


Genetic Basis for Metabolism of Methylated Sulfur Compounds in Methanosarcina Species
journal, February 2015

  • Fu, He; Metcalf, William W.
  • Journal of Bacteriology, Vol. 197, Issue 8
  • DOI: 10.1128/JB.02605-14

Biosynthesis of the Thiazole Moiety of Thiamin Pyrophosphate (Vitamin B1)
journal, October 2003

  • Park, Joo-Heon; Dorrestein, Pieter C.; Zhai, Huili
  • Biochemistry, Vol. 42, Issue 42
  • DOI: 10.1021/bi034902z

Molecular, genetic, and biochemical characterization of the serC gene of Methanosarcina barkeri Fusaro.
journal, October 1996


Mode of action of closthioamide: the first member of the polythioamide class of bacterial DNA gyrase inhibitors
journal, July 2015

  • Chiriac, Alina Iulia; Kloss, Florian; Krämer, Jonas
  • Journal of Antimicrobial Chemotherapy, Vol. 70, Issue 9
  • DOI: 10.1093/jac/dkv161

Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature
journal, January 2013

  • Arnison, Paul G.; Bibb, Mervyn J.; Bierbaum, Gabriele
  • Nat. Prod. Rep., Vol. 30, Issue 1
  • DOI: 10.1039/C2NP20085F

ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process
journal, November 2011

  • Basu, Malay K.; Selengut, Jeremy D.; Haft, Daniel H.
  • BMC Bioinformatics, Vol. 12, Issue 1
  • DOI: 10.1186/1471-2105-12-434

The origin and evolution of Archaea: a state of the art
journal, May 2006

  • Gribaldo, Simonetta; Brochier-Armanet, Celine
  • Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 361, Issue 1470
  • DOI: 10.1098/rstb.2006.1841

The key nickel enzyme of methanogenesis catalyses the anaerobic oxidation of methane
journal, June 2010

  • Scheller, Silvan; Goenrich, Meike; Boecher, Reinhard
  • Nature, Vol. 465, Issue 7298
  • DOI: 10.1038/nature09015

Direct evidence for enzyme persulfide and disulfide intermediates during 4-thiouridine biosynthesis
journal, January 2006

  • Wright, Chapman M.; Christman, Glenn D.; Snellinger, Ann M.
  • Chemical Communications, Issue 29
  • DOI: 10.1039/b604040c

Methanogenic archaea: ecologically relevant differences in energy conservation
journal, June 2008

  • Thauer, Rudolf K.; Kaster, Anne-Kristin; Seedorf, Henning
  • Nature Reviews Microbiology, Vol. 6, Issue 8
  • DOI: 10.1038/nrmicro1931

Didehydroaspartate Modification in Methyl-Coenzyme M Reductase Catalyzing Methane Formation
journal, July 2016

  • Wagner, Tristan; Kahnt, Jörg; Ermler, Ulrich
  • Angewandte Chemie International Edition, Vol. 55, Issue 36
  • DOI: 10.1002/anie.201603882

Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota
journal, October 2016


YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function
journal, March 2017


The universal tree of life: an update
journal, July 2015


Control of Plant Defense Mechanisms and Fire Blight Pathogenesis through the Regulation of 6-Thioguanine Biosynthesis in Erwinia amylovora
journal, January 2014

  • Coyne, Sébastien; Litomska, Agnieszka; Chizzali, Cornelia
  • ChemBioChem, Vol. 15, Issue 3
  • DOI: 10.1002/cbic.201300684

MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004

  • Edgar, R. C.
  • Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
  • DOI: 10.1093/nar/gkh340

Why Does Thioformamide Have a Larger Rotational Barrier Than Formamide?
journal, March 1995

  • Wiberg, Kenneth B.; Rablen, Paul R.
  • Journal of the American Chemical Society, Vol. 117, Issue 8
  • DOI: 10.1021/ja00113a009

On the use of thioamides as fluorescence quenching probes for tracking protein folding and stability
journal, January 2014

  • Petersson, E. James; Goldberg, Jacob M.; Wissner, Rebecca F.
  • Phys. Chem. Chem. Phys., Vol. 16, Issue 15
  • DOI: 10.1039/C3CP55525A

Phylogenomic Data Support a Seventh Order of Methylotrophic Methanogens and Provide Insights into the Evolution of Methanogenesis
journal, August 2013

  • Borrel, Guillaume; O’Toole, Paul W.; Harris, Hugh M. B.
  • Genome Biology and Evolution, Vol. 5, Issue 10
  • DOI: 10.1093/gbe/evt128

Cas9-mediated genome editing in the methanogenic archaeon Methanosarcina acetivorans
journal, March 2017

  • Nayak, Dipti D.; Metcalf, William W.
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 11
  • DOI: 10.1073/pnas.1618596114

Analysis of Protein Stability and Ligand Interactions by Thermal Shift Assay
journal, February 2015


Temperature dependence of methyl-coenzyme M reductase activity and of the formation of the methyl-coenzyme M reductase red2 state induced by coenzyme B
journal, April 2005

  • Goenrich, Meike; Duin, Evert C.; Mahlert, Felix
  • JBIC Journal of Biological Inorganic Chemistry, Vol. 10, Issue 4
  • DOI: 10.1007/s00775-005-0636-6

An Anaerobic, Intrachamber Incubator for Growth ofMethanosarcina spp. on Methanol-Containing Solid Media
journal, January 1998

  • Metcalf, William W.; Zhang, Jun Kai; Wolfe, Ralph S.
  • Applied and Environmental Microbiology, Vol. 64, Issue 2
  • DOI: 10.1128/AEM.64.2.768-770.1998

Disaggregation of Methanosarcina spp. and Growth as Single Cells at Elevated Osmolarity
journal, January 1993


    Works referencing / citing this record:

    Ynamide-Mediated Thiopeptide Synthesis
    journal, January 2019


    Dithioamide substitutions in proteins: effects on thermostability, peptide binding, and fluorescence quenching in calmodulin
    journal, January 2018

    • Walters, Christopher R.; Ferrie, John J.; Petersson, E. James
    • Chemical Communications, Vol. 54, Issue 14
    • DOI: 10.1039/c8cc00104a

    The biosynthesis of methanobactin
    journal, March 2018

    • Kenney, Grace E.; Dassama, Laura M. K.; Pandelia, Maria-Eirini
    • Science, Vol. 359, Issue 6382
    • DOI: 10.1126/science.aap9437

    Insights into the thioamidation of thiopeptins to enhance the understanding of the biosynthetic logic of thioamide-containing thiopeptides
    journal, January 2019

    • Liu, Jingyu; Lin, Zhi; Li, Yuqing
    • Organic & Biomolecular Chemistry, Vol. 17, Issue 15
    • DOI: 10.1039/c9ob00402e

    The streptothricin acetyltransferase (sat) gene as a positive selectable marker for methanogenic archaea
    journal, September 2019

    • Farley, Kristen R.; Metcalf, William W.
    • FEMS Microbiology Letters, Vol. 366, Issue 17
    • DOI: 10.1093/femsle/fnz216

    Methanogenesis marker protein 10 (Mmp10) from Methanosarcina acetivorans is a radical S -adenosylmethionine methylase that unexpectedly requires cobalamin
    journal, May 2019

    • Radle, Matthew I.; Miller, Danielle V.; Laremore, Tatiana N.
    • Journal of Biological Chemistry, Vol. 294, Issue 31
    • DOI: 10.1074/jbc.ra119.007609

    Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea
    journal, March 2019


    Enzymatic reconstitution of ribosomal peptide backbone thioamidation
    journal, March 2018

    • Mahanta, Nilkamal; Liu, Andi; Dong, Shihui
    • Proceedings of the National Academy of Sciences, Vol. 115, Issue 12
    • DOI: 10.1073/pnas.1722324115

    Enzymatic Thioamide Formation in a Bacterial Antimetabolite Pathway
    journal, August 2018

    • Litomska, Agnieszka; Ishida, Keishi; Dunbar, Kyle L.
    • Angewandte Chemie, Vol. 130, Issue 36
    • DOI: 10.1002/ange.201804158

    Increasing the bioactive space of peptide macrocycles by thioamide substitution
    journal, January 2018

    • Verma, Hitesh; Khatri, Bhavesh; Chakraborti, Sohini
    • Chemical Science, Vol. 9, Issue 9
    • DOI: 10.1039/c7sc04671e

    Reconstitution of Iterative Thioamidation in Closthioamide Biosynthesis Reveals Tailoring Strategy for Nonribosomal Peptide Backbones
    journal, August 2019

    • Dunbar, Kyle L.; Dell, Maria; Molloy, Evelyn M.
    • Angewandte Chemie International Edition, Vol. 58, Issue 37
    • DOI: 10.1002/anie.201905992

    Genome Editing Reveals Novel Thiotemplated Assembly of Polythioamide Antibiotics in Anaerobic Bacteria
    journal, October 2018

    • Dunbar, Kyle L.; Büttner, Hannah; Molloy, Evelyn M.
    • Angewandte Chemie, Vol. 130, Issue 43
    • DOI: 10.1002/ange.201807970