Complete genome sequence of Methanospirillum hungatei type strain JF1

Gunsalus, Robert; Cook, Lauren E.; Crable, Bryan R.; Rohlin, Lars; McDonald, Erin; Mouttaki, Housna; Sieber, Jessica R.; Poweleit, Nicole; Zhou, Hong; Lapidus, Alla; Daligault, Hajnalka E.; Land, Miriam L.; Gilna, Paul; Ivanova, Natalia; Kyripides, Nikos; Culley, David E.; McInerney, Michael J.

doi:10.1186/s40793-015-0124-8

Title: Complete genome sequence of Methanospirillum hungatei type strain JF1

Abstract

Methanospirillum hungatei strain JF1 is a hydrogenotrophic methanogen that belongs to the order Methanomicrobiales. Members of the genus Methanospirillum are commonly encountered in syntrophic association with fermenting microorganisms. M. hungatei serves as the model partner organism in laboratory cocultures that syntrophically oxidize fatty and aromatic acids. Furthermore, when grown syntrophically, M. hungatei rapidly uses the hydrogen or formate produced by its syntrophic partner and maintains the concentration of these metabolites at very low levels so that the degradation of the syntrophic substrate is thermodynamically favorable.

Authors:

Gunsalus, Robert ^[1]; Cook, Lauren E. ^[2]; Crable, Bryan R. ^[3]; Rohlin, Lars ^[2]; McDonald, Erin ^[2]; Mouttaki, Housna ^[4]; Sieber, Jessica R. ^[3]; Poweleit, Nicole ^[2]; Zhou, Hong ^[2]; Lapidus, Alla ^[5]; Daligault, Hajnalka E. ^[6]; Land, Miriam L. ^[7]; Gilna, Paul ^[7]; Ivanova, Natalia ^[8]; Kyripides, Nikos ^[9]; Culley, David E. ^[10]; McInerney, Michael J. ^[3]

Univ. of California, Los Angeles, CA (United States). Dept. of Microbiology, Immunology, and Molecular Genetics; Univ. of California, Los Angeles, CA (United States). UCLA-DOE Institute for Genomics and Proteomics
Univ. of California, Los Angeles, CA (United States). Dept. of Microbiology, Immunology, and Molecular Genetics
Univ. of Oklahoma, Norman, OK (United States)
Univ. of California, Los Angeles, CA (United States). Dept. of Microbiology, Immunology, and Molecular Genetics; Univ. of Oklahoma, Norman, OK (United States)
St. Petersburg State University, St. Petersburg (Russia); St. Petersburg Academic University, St. Petersburg (Russia)
St. Petersburg State University, St. Petersburg (Russia)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
DOE Joint Genome Institute, Walnut Creek, CA (United States)
DOE Joint Genome Institute, Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

Publication Date:: Wed Jan 06 00:00:00 EST 2016

Research Org.:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Univ. of Oklahoma, Norman, OK (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Biological and Environmental Research (BER); Work for Others (WFO); USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences, and Biosciences Division

OSTI Identifier:: 1243176

Alternate Identifier(s):: OSTI ID: 1265977; OSTI ID: 1604953

Report Number(s):: PNNL-SA-100776
Journal ID: ISSN 1944-3277; BM0101020

Grant/Contract Number:: AC05-76RL01830; FG02-96ER20214; FG03-86ER13498; FC02-02ER63421; AC05-00OR22725

Resource Type:: Accepted Manuscript

Journal Name:: Standards in Genomic Sciences

Additional Journal Information:: Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 1944-3277

Publisher:: BioMed Central

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES; syntrophy; biohydrogen; methanogeneis; biofuels; hydrogenase; formate dehydrogenase; bioenergetics; fatty acids; syntrophic partnerships; Methanomicrobiales; anaerobic; motile; methangenic; hydrogen; Methangenic archaea; formate

Citation Formats


                    Gunsalus, Robert, Cook, Lauren E., Crable, Bryan R., Rohlin, Lars, McDonald, Erin, Mouttaki, Housna, Sieber, Jessica R., Poweleit, Nicole, Zhou, Hong, Lapidus, Alla, Daligault, Hajnalka E., Land, Miriam L., Gilna, Paul, Ivanova, Natalia, Kyripides, Nikos, Culley, David E., and McInerney, Michael J. Complete genome sequence of Methanospirillum hungatei type strain JF1.  United States: N. p., 2016. 
Web.  doi:10.1186/s40793-015-0124-8.

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                    Gunsalus, Robert, Cook, Lauren E., Crable, Bryan R., Rohlin, Lars, McDonald, Erin, Mouttaki, Housna, Sieber, Jessica R., Poweleit, Nicole, Zhou, Hong, Lapidus, Alla, Daligault, Hajnalka E., Land, Miriam L., Gilna, Paul, Ivanova, Natalia, Kyripides, Nikos, Culley, David E., & McInerney, Michael J. Complete genome sequence of Methanospirillum hungatei type strain JF1.  United States.  https://doi.org/10.1186/s40793-015-0124-8

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                    Gunsalus, Robert, Cook, Lauren E., Crable, Bryan R., Rohlin, Lars, McDonald, Erin, Mouttaki, Housna, Sieber, Jessica R., Poweleit, Nicole, Zhou, Hong, Lapidus, Alla, Daligault, Hajnalka E., Land, Miriam L., Gilna, Paul, Ivanova, Natalia, Kyripides, Nikos, Culley, David E., and McInerney, Michael J. Wed .  
"Complete genome sequence of Methanospirillum hungatei type strain JF1".  United States.  https://doi.org/10.1186/s40793-015-0124-8.  https://www.osti.gov/servlets/purl/1243176.

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@article{osti_1243176,

  title        = {Complete genome sequence of Methanospirillum hungatei type strain JF1},

  author       = {Gunsalus, Robert and Cook, Lauren E. and Crable, Bryan R. and Rohlin, Lars and McDonald, Erin and Mouttaki, Housna and Sieber, Jessica R. and Poweleit, Nicole and Zhou, Hong and Lapidus, Alla and Daligault, Hajnalka E. and Land, Miriam L. and Gilna, Paul and Ivanova, Natalia and Kyripides, Nikos and Culley, David E. and McInerney, Michael J.},

  abstractNote = {Methanospirillum hungatei strain JF1 is a hydrogenotrophic methanogen that belongs to the order Methanomicrobiales. Members of the genus Methanospirillum are commonly encountered in syntrophic association with fermenting microorganisms. M. hungatei serves as the model partner organism in laboratory cocultures that syntrophically oxidize fatty and aromatic acids. Furthermore, when grown syntrophically, M. hungatei rapidly uses the hydrogen or formate produced by its syntrophic partner and maintains the concentration of these metabolites at very low levels so that the degradation of the syntrophic substrate is thermodynamically favorable.},

  doi          = {10.1186/s40793-015-0124-8},

  journal      = {Standards in Genomic Sciences},

  number       = 1,

  volume       = 11,

  place        = {United States},

  year         = {Wed Jan 06 00:00:00 EST 2016},

  month        = {Wed Jan 06 00:00:00 EST 2016}

}

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https://doi.org/10.1186/s40793-015-0124-8

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We report the complete genome sequence of Methanospirillum hungatei strain GP1 (DSM 1101). Strain GP1 oxidizes H ₂ , formate, and secondary alcohols as the substrates for methanogenesis. Members of the genus are model organisms used to study syntrophic growth with bacterial partners, but secondary alcohol metabolism remains poorly studied.
https://doi.org/10.1128/MRA.00708-21
Membrane Complexes of Syntrophomonas wolfei Involved in Syntrophic Butyrate Degradation and Hydrogen Formation

Journal Article Crable, Bryan R. ; Sieber, Jessica R. ; Mao, Xinwei ; ... - Frontiers in Microbiology

Syntrophic butyrate metabolism involves the thermodynamically unfavorable production of hydrogen and/or formate from the high potential electron donor, butyryl-CoA. Such redox reactions can occur only with energy input by a process called reverse electron transfer. Previous studies have demonstrated that hydrogen production from butyrate requires the presence of a proton gradient, but the biochemical machinery involved has not been clearly elucidated. In this study, the gene and enzyme systems involved in reverse electron transfer by Syntrophomonas wolfei were investigated using proteomic and gene expression approaches. S. wolfei was grown in coculture with Methanospirillum hungatei or Dehalococcoides mccartyi under conditions requiringmore »« less
Cited by 23
https://doi.org/10.3389/fmicb.2016.01795

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Palladium-mediated hydrogenation of unsaturated hydrocarbons with hydrogen gas released during anaerobic cellulose degradation. [Neocallimastix frontalis; Ruminococcus albus; methanospirillum hungatei]

Journal Article Mountfort, D O ; Kaspar, H F - Appl. Environ. Microbiol.; (United States)

Among five hydrogenation catalysts, palladium on charcoal was the most reactive one when suspended in anaerobic culture medium, and Lindlar catalyst (Pd on CaCO/sub 3/) was the most reactive one when suspended in the gas phase of culture tubes. Palladium on charcoal in the culture medium (40 to 200 mg 10 ml/sup -1/) completely inhibited growth of Neocallimastix frontalis and partly inhibited Ruminococcus albus. Lindlar catalyst (40 to 200 mg per tube) suspended in a glass pouch above the culture medium did not affect the rate of cellulose degradation or the ration of fermentation products by these organisms. Acetylene addedmore »« less
Proteomic analysis reveals metabolic and regulatory systems involved in the syntrophic and axenic lifestyle of Syntrophomonas wolfei

Journal Article Sieber, Jessica R. ; Crable, Bryan R. ; Sheik, Cody S. ; ... - Frontiers in Microbiology

Microbial syntrophy is a vital metabolic interaction necessary for the complete oxidation of organic biomass to methane in all-anaerobic ecosystems. However, this process is thermodynamically constrained and represents an ecosystem-level metabolic bottleneck. To gain insight into the physiology of this process, a shotgun proteomics approach was used to quantify the protein landscape of the model syntrophic metabolizer, Syntrophomonas wolfei, grown axenically and syntrophically with Methanospirillum hungatei. Remarkably, the abundance of most proteins as represented by normalized spectral abundance factor (NSAF) value changed very little between the pure and coculture growth conditions. Among the most abundant proteins detected were GroEL andmore »« less
Cited by 37
https://doi.org/10.3389/fmicb.2015.00115

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Syntrophus aciditrophicus uses the same enzymes in a reversible manner to degrade and synthesize aromatic and alicyclic acids

Journal Article James, Kimberly L. ; Kung, Johannes W. ; Crable, Bryan R. ; ... - Environmental Microbiology

We report that syntrophy is essential for the efficient conversion of organic carbon to methane in natural and constructed environments, but little is known about the enzymes involved in syntrophic carbon and electron flow. Syntrophus aciditrophicus strain SB syntrophically degrades benzoate and cyclohexane-1-carboxylate and catalyzes the novel synthesis of benzoate and cyclohexane-1-carboxylate from crotonate. We used proteomic, biochemical, and metabolomic approaches to determine what enzymes are used for fatty, aromatic, and alicyclic acid degradation versus for benzoate and cyclohexane-1-carboxylate synthesis. Enzymes involved in the metabolism of cyclohex-1,5-diene carboxyl-CoA to acetyl-CoA were in high abundance in S. aciditrophicus cells grown inmore »« less
Cited by 10
https://doi.org/10.1111/1462-2920.14601

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