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Title: Deciphering mixotrophic Clostridium formicoaceticum metabolism and energy conservation: Genomic analysis and experimental studies

Abstract

Clostridium formicoaceticum, a Gram-negative mixotrophic homoacetogen, produces acetic acid as the sole metabolic product from various carbon sources, including fructose, glycerol, formate, and CO2. Its genome of 4.59-Mbp contains a highly conserved Wood-Ljungdahl pathway gene cluster with the same layout as that in other mixotrophic acetogens, including Clostridium aceticum, Clostridium carboxidivorans, and Clostridium ljungdahlii. For energy conservation, C. formicoaceticum does not have all the genes required for the synthesis of cytochrome or quinone used for generating proton gradient in H+-dependent acetogens such as Moorella thermoacetica; instead, it has the Rnf system and a Na+-translocating ATPase similar to the one in Acetobacterium woodii. Furthermore its growth in both heterotrophic and autotrophic media were dependent on the sodium concentration. C. formicoaceticum has genes encoding acetaldehyde dehydrogenases, alcohol dehydrogenases, and aldehyde oxidoreductases, which could convert acetyl-CoA and acetate to ethanol and butyrate to butanol under excessive reducing equivalent conditions.

Authors:
 [1]; ORCiD logo [1];  [1];  [2];  [3]; ORCiD logo [1]
  1. The Ohio State Univ., Columbus, OH (United States)
  2. South China Univ. of Technology, Guangzhou (China)
  3. Zhejiang Univ., Zhejiang (China)
Publication Date:
Research Org.:
The Ohio State Univ., Columbus, OH (United States)
Sponsoring Org.:
USDOE Office of Energy Efficiency and Renewable Energy (EERE), Transportation Office. Bioenergy Technologies Office
OSTI Identifier:
1572178
Grant/Contract Number:  
EE0007005
Resource Type:
Accepted Manuscript
Journal Name:
Genomics
Additional Journal Information:
Journal Volume: 111; Journal Issue: 6; Journal ID: ISSN 0888-7543
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; Acetate; Acetogen; Clostridium formicoaceticum; Genomic analysis; Mixotrophy; Wood-Ljungdahl pathway

Citation Formats

Bao, Teng, Cheng, Chi, Xin, Xin, Wang, Jufang, Wang, Mingqi, and Yang, Shang-Tian. Deciphering mixotrophic Clostridium formicoaceticum metabolism and energy conservation: Genomic analysis and experimental studies. United States: N. p., 2018. Web. doi:10.1016/j.ygeno.2018.11.020.
Bao, Teng, Cheng, Chi, Xin, Xin, Wang, Jufang, Wang, Mingqi, & Yang, Shang-Tian. Deciphering mixotrophic Clostridium formicoaceticum metabolism and energy conservation: Genomic analysis and experimental studies. United States. https://doi.org/10.1016/j.ygeno.2018.11.020
Bao, Teng, Cheng, Chi, Xin, Xin, Wang, Jufang, Wang, Mingqi, and Yang, Shang-Tian. Tue . "Deciphering mixotrophic Clostridium formicoaceticum metabolism and energy conservation: Genomic analysis and experimental studies". United States. https://doi.org/10.1016/j.ygeno.2018.11.020. https://www.osti.gov/servlets/purl/1572178.
@article{osti_1572178,
title = {Deciphering mixotrophic Clostridium formicoaceticum metabolism and energy conservation: Genomic analysis and experimental studies},
author = {Bao, Teng and Cheng, Chi and Xin, Xin and Wang, Jufang and Wang, Mingqi and Yang, Shang-Tian},
abstractNote = {Clostridium formicoaceticum, a Gram-negative mixotrophic homoacetogen, produces acetic acid as the sole metabolic product from various carbon sources, including fructose, glycerol, formate, and CO2. Its genome of 4.59-Mbp contains a highly conserved Wood-Ljungdahl pathway gene cluster with the same layout as that in other mixotrophic acetogens, including Clostridium aceticum, Clostridium carboxidivorans, and Clostridium ljungdahlii. For energy conservation, C. formicoaceticum does not have all the genes required for the synthesis of cytochrome or quinone used for generating proton gradient in H+-dependent acetogens such as Moorella thermoacetica; instead, it has the Rnf system and a Na+-translocating ATPase similar to the one in Acetobacterium woodii. Furthermore its growth in both heterotrophic and autotrophic media were dependent on the sodium concentration. C. formicoaceticum has genes encoding acetaldehyde dehydrogenases, alcohol dehydrogenases, and aldehyde oxidoreductases, which could convert acetyl-CoA and acetate to ethanol and butyrate to butanol under excessive reducing equivalent conditions.},
doi = {10.1016/j.ygeno.2018.11.020},
journal = {Genomics},
number = 6,
volume = 111,
place = {United States},
year = {2018},
month = {11}
}

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Works referenced in this record:

Clostridium autoethanogenum, sp. nov., an anaerobic bacterium that produces ethanol from carbon monoxide
journal, April 1994

  • Abrini, Jamal; Naveau, Henry; Nyns, Edmond-Jacques
  • Archives of Microbiology, Vol. 161, Issue 4
  • DOI: 10.1007/BF00303591

Clostridium formicoaceticum nov. spec. Isolation, description and distinction from C. aceticum and C. thermoaceticum
journal, January 1970

  • Andreesen, J. R.; Gottschalk, G.; Schlegel, H. G.
  • Archiv f�r Mikrobiologie, Vol. 72, Issue 2
  • DOI: 10.1007/BF00409521

Design and analysis of metabolic pathways supporting formatotrophic growth for electricity-dependent cultivation of microbes
journal, August 2013

  • Bar-Even, Arren; Noor, Elad; Flamholz, Avi
  • Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1827, Issue 8-9
  • DOI: 10.1016/j.bbabio.2012.10.013

CO Metabolism in the Acetogen Acetobacterium woodii
journal, September 2015

  • Bertsch, Johannes; Müller, Volker
  • Applied and Environmental Microbiology, Vol. 81, Issue 17
  • DOI: 10.1128/AEM.01772-15

Purification and properties of 5,10-methylenetetrahydrofolate reductase, an iron-sulfur flavoprotein from Clostridium formicoaceticum.
journal, September 1984


Identifying bacterial genes and endosymbiont DNA with Glimmer
journal, January 2007


Fermentation of fumarate and L-malate by Clostridium formicoaceticum
journal, January 1978


Ancestral sporulation initiation: Ancestral sporulation initiation
journal, March 2011


Growth of Eubacterium limosum with Carbon Monoxide as the Energy Source
journal, January 1982


Presence of Cytochrome and Menaquinone in Clostridium formicoaceticum and Clostridium thermoaceticum
journal, January 1975


CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats
journal, May 2007

  • Grissa, I.; Vergnaud, G.; Pourcel, C.
  • Nucleic Acids Research, Vol. 35, Issue Web Server
  • DOI: 10.1093/nar/gkm360

Acetone production with metabolically engineered strains of Acetobacterium woodii
journal, July 2016


Acetic Acid Production from Fructose by Clostridium formicoaceticum Immobilized in a Fibrous-Bed Bioreactor
journal, October 1998

  • Huang, Y. L.; Mann, K.; Novak, J. M.
  • Biotechnology Progress, Vol. 14, Issue 5
  • DOI: 10.1021/bp980077f

Energy Conservation Model Based on Genomic and Experimental Analyses of a Carbon Monoxide-Utilizing, Butyrate-Forming Acetogen, Eubacterium limosum KIST612
journal, July 2015

  • Jeong, Jiyeong; Bertsch, Johannes; Hess, Verena
  • Applied and Environmental Microbiology, Vol. 81, Issue 14
  • DOI: 10.1128/AEM.00675-15

CO2 fixation by anaerobic non-photosynthetic mixotrophy for improved carbon conversion
journal, September 2016

  • Jones, Shawn W.; Fast, Alan G.; Carlson, Ellinor D.
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms12800

Complete Genome Sequence of the Autotrophic Acetogen Clostridium formicaceticum DSM 92 T Using Nanopore and Illumina Sequencing Data
journal, May 2017

  • Karl, Michael M.; Poehlein, Anja; Bengelsdorf, Frank R.
  • Genome Announcements, Vol. 5, Issue 21
  • DOI: 10.1128/genomeA.00423-17

Clostridium ljungdahlii represents a microbial production platform based on syngas
journal, July 2010

  • Kopke, M.; Held, C.; Hujer, S.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 29, p. 13087-13092
  • DOI: 10.1073/pnas.1004716107

RNAmmer: consistent and rapid annotation of ribosomal RNA genes
journal, April 2007

  • Lagesen, Karin; Hallin, Peter; Rødland, Einar Andreas
  • Nucleic Acids Research, Vol. 35, Issue 9
  • DOI: 10.1093/nar/gkm160

A Genetic System for Clostridium ljungdahlii: a Chassis for Autotrophic Production of Biocommodities and a Model Homoacetogen
journal, November 2012

  • Leang, Ching; Ueki, Toshiyuki; Nevin, Kelly P.
  • Applied and Environmental Microbiology, Vol. 79, Issue 4
  • DOI: 10.1128/AEM.02891-12

Recovery and Analysis of Formyltetrahydrofolate Synthetase Gene Sequences from Natural Populations of Acetogenic Bacteria
journal, March 2001


Screening for plasmids in the genus Clostridium
journal, July 1987

  • Lee, C. -K.; D�rre, P.; Hippe, H.
  • Archives of Microbiology, Vol. 148, Issue 2
  • DOI: 10.1007/BF00425357

tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence
journal, March 1997


Structural Investigations of the Membrane-Embedded Rotor Ring of the F-ATPase from Clostridium paradoxum
journal, September 2006

  • Meier, T.; Ferguson, S. A.; Cook, G. M.
  • Journal of Bacteriology, Vol. 188, Issue 22
  • DOI: 10.1128/JB.00934-06

Evidence for a Hexaheteromeric Methylenetetrahydrofolate Reductase in Moorella thermoacetica
journal, July 2014

  • Mock, J.; Wang, S.; Huang, H.
  • Journal of Bacteriology, Vol. 196, Issue 18
  • DOI: 10.1128/JB.01839-14

Purification and Characterization of Nicotinamide Adenine Dinucleotide-dependent Methylenetetrahydrofolate Dehydrogenase from Clostridium formicoaceticum
journal, August 1974

  • Moore, Michael R.; O'Brien, William E.; Ljungdahl, Lars G.
  • Journal of Biological Chemistry, Vol. 249, Issue 16
  • DOI: 10.1016/S0021-9258(19)42355-7

Energy Conservation in Acetogenic Bacteria
journal, November 2003


Rfam 12.0: updates to the RNA families database
journal, November 2014

  • Nawrocki, Eric P.; Burge, Sarah W.; Bateman, Alex
  • Nucleic Acids Research, Vol. 43, Issue D1
  • DOI: 10.1093/nar/gku1063

Fermentation of Fructose and Synthesis of Acetate from Carbon Dioxide by Clostridium formicoaceticum
journal, February 1972


The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum)
journal, July 2008


The Complete Genome Sequence of Clostridium aceticum: a Missing Link between Rnf- and Cytochrome-Containing Autotrophic Acetogens
journal, September 2015


An Ancient Pathway Combining Carbon Dioxide Fixation with the Generation and Utilization of a Sodium Ion Gradient for ATP Synthesis
journal, March 2012


Acetogenesis and the Wood–Ljungdahl pathway of CO2 fixation
journal, December 2008

  • Ragsdale, Stephen W.; Pierce, Elizabeth
  • Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1784, Issue 12, p. 1873-1898
  • DOI: 10.1016/j.bbapap.2008.08.012

The Na+-F1F0-ATPase Operon from Acetobacterium woodii
journal, November 1999

  • Rahlfs, Stefan; Aufurth, Sascha; Müller, Volker
  • Journal of Biological Chemistry, Vol. 274, Issue 48
  • DOI: 10.1074/jbc.274.48.33999

Effects of pH and acetic acid on homoacetic fermentation of lactate byClostridium formicoaceticum
journal, October 1989

  • Tang, I-Ching; Okos, Martin R.; Yang, Shang-Tian
  • Biotechnology and Bioengineering, Vol. 34, Issue 8
  • DOI: 10.1002/bit.260340807

Acetic acid production from whey lactose by the co-culture ofStreptococcus lactis andClostridium formicoaceticum
journal, April 1988

  • Tang, I-Ching; Yang, Shang-Tian; Okos, Martin R.
  • Applied Microbiology and Biotechnology, Vol. 28, Issue 2
  • DOI: 10.1007/BF00694301

Motility and Flagellar Glycosylation in Clostridium difficile
journal, September 2009

  • Twine, Susan M.; Reid, Christopher W.; Aubry, Annie
  • Journal of Bacteriology, Vol. 191, Issue 22
  • DOI: 10.1128/JB.00861-09

Engineering clostridia for butanol production from biorenewable resources: from cells to process integration
journal, November 2014


A novel mode of lactate metabolism in strictly anaerobic bacteria: A novel mode of lactate metabolism in anaerobes
journal, May 2014

  • Weghoff, Marie Charlotte; Bertsch, Johannes; Müller, Volker
  • Environmental Microbiology, Vol. 17, Issue 3
  • DOI: 10.1111/1462-2920.12493

On a reversible molybdenum-containing aldehyde oxidoreductase from Clostridium formicoaceticum
journal, March 1993

  • White, Hiltrud; Huber, Claudia; Feicht, Richard
  • Archives of Microbiology, Vol. 159, Issue 3
  • DOI: 10.1007/BF00248479

Kinetics of Homoacetic Fermentation of Lactate by Clostridium formicoaceticum
journal, April 1987


Anaerobic fermentation of glycerol: a path to economic viability for the biofuels industry
journal, June 2007


Ethanol and acetate production from synthesis gas via fermentation processes using anaerobic bacterium, Clostridium ljungdahlii
journal, December 2005

  • Younesi, Habibollah; Najafpour, Ghasem; Mohamed, Abdul Rahman
  • Biochemical Engineering Journal, Vol. 27, Issue 2, p. 110-119
  • DOI: 10.1016/j.bej.2005.08.015

Metabolic engineering of Clostridium tyrobutyricum for n-butanol production through co-utilization of glucose and xylose : Metabolic Engineering of
journal, June 2015

  • Yu, Le; Xu, Mengmeng; Tang, I-Ching
  • Biotechnology and Bioengineering, Vol. 112, Issue 10
  • DOI: 10.1002/bit.25613

Works referencing / citing this record:

Engineering Clostridium for improved solvent production: recent progress and perspective
journal, May 2019

  • Cheng, Chi; Bao, Teng; Yang, Shang-Tian
  • Applied Microbiology and Biotechnology, Vol. 103, Issue 14
  • DOI: 10.1007/s00253-019-09916-7