Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model

Islam, M. Ahsanul; Zengler, Karsten; Edwards, Elizabeth A.; Mahadevan, Radhakrishnan; Stephanopoulos, Gregory

doi:10.1039/c5ib00095e

Cited by 41Microbial Metabolic Engineering and BioproductionGene Regulatory Network AnalysisBioinformatics and Genomic Networks

Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model

Open access

Islam, M. Ahsanul, Zengler, Karsten, Edwards, Elizabeth A., Mahadevan, Radhakrishnan, Stephanopoulos, Gregory·2015·Integrative Biology

DOI 10.1039/c5ib00095e

Open this paper in CoChat — free account

Abstract

Moorella thermoacetica is a strictly anaerobic, endospore-forming, and metabolically versatile acetogenic bacterium capable of conserving energy by both autotrophic (acetogenesis) and heterotrophic (homoacetogenesis) modes of metabolism. Its metabolic diversity and the ability to efficiently convert a wide range of compounds, including syngas (CO + H2) into acetyl-CoA have made this thermophilic bacterium a promising host for industrial biotechnology applications. However, lack of detailed information on M. thermoacetica's metabolism is a major impediment to its use as a microbial cell factory. In order to overcome this issue, a genome-scale constraint-based metabolic model of Moorella thermoacetica, iAI558, has been developed using its genome sequence and physiological data from published literature. The reconstructed metabolic network of M. thermoacetica comprises 558 metabolic genes, 705 biochemical reactions, and 698 metabolites. Of the total 705 model reactions, 680 are gene-associated while the rest are non-gene associated reactions. The model, in addition to simulating both autotrophic and heterotrophic growth of M. thermoacetica, revealed degeneracy in its TCA-cycle, a common characteristic of anaerobic metabolism. Furthermore, the model helped elucidate the poorly understood energy conservation mechanism of M. thermoacetica during autotrophy. Thus, in addition to generating experimentally testable hypotheses regarding its physiology, such a detailed model will facilitate rapid strain designing and metabolic engineering of M. thermoacetica for industrial applications.

Integrity signals

Registry

Crossref · 10.1039/c5ib00095e

Cites

57 of 57 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Similar genome-scale models also exist for C. ljungdahlii and M. thermoacetica.
“Similar models also exist for C. ljungdahlii (Nagarajan et al., 2013) and M. thermoacetica (Islam et al., 2015).”
From Gas Fermentation—A Flexible Platform for Commercial Scale Production of Low-Carbon-Fuels and Chemicals from Waste and Renewable Feedstocks (2016) · cites this paper as Islam et al., 2015

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302 · see citing works
The RAST Server: Rapid Annotations using Subsystems Technology
Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T. L., Edwards, R. A., Formsma, K., Gerdes, S., Glass, E. M., Kubal, M., et al. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-75 · Cited by 11,777 · see citing works
Circos: An information aesthetic for comparative genomicsPreprint
Krzywinski, M. I., Schein, J. E., Birol, İ., Connors, J. M., Gascoyne, R. D., Horsman, D. E., Jones, S. J. M., & Marra, M. A. (2009) · Genome Research · doi:10.1101/gr.092759.109 · Cited by 10,838 · see citing works
Brock Biology of Microorganisms
Madigan, M. T., Bender, K. S., Buckley, D. H., Sattley, W. M., & Stahl, D. A. (1996) · Cited by 5,759 · see citing works
Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism
MITCHELL, P. (1961) · Nature · doi:10.1038/191144a0 · Cited by 4,704 · see citing works
What is flux balance analysis?
Orth, J. D., Thiele, I., & Palsson, B. Ø. (2010) · Nature Biotechnology · doi:10.1038/nbt.1614 · Cited by 3,903 · see citing works
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
Overbeek, R. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki866 · Cited by 2,019 · see citing works
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., et al. (2011) · Nature Protocols · doi:10.1038/nprot.2011.308 · Cited by 1,835 · see citing works
A protocol for generating a high-quality genome-scale metabolic reconstruction
Thiele, I., & Palsson, B. Ø. (2010) · Nature Protocols · doi:10.1038/nprot.2009.203 · Cited by 1,789 · see citing works
The Phylogeny of the Genus Clostridium: Proposal of Five New Genera and Eleven New Species Combinations
Collins, M. D., Lawson, P. A., Willems, A. L., Córdoba, J. J., Fernández‐Garayzábal, J. F., GARCIA, P., Cai, J., Hippe, H., & Farrow, J. A. E. (1994) · International Journal of Systematic Bacteriology · doi:10.1099/00207713-44-4-812 · Cited by 1,670 · see citing works
Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles
Pellegrini, M. A., Marcotte, E. M., Thompson, M. J., Eisenberg, D. S., & Yeates, T. O. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.8.4285 · Cited by 1,568 · see citing works
Acetogenesis and the Wood–Ljungdahl pathway of CO2 fixation
Ragsdale, S. W., & Pierce, E. (2008) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2008.08.012 · Cited by 1,337 · see citing works
IMG: the integrated microbial genomes database and comparative analysis system
Markowitz, V. M., Chen, I.-M. A., Palaniappan, K., Chu, K., Szeto, E., Grechkin, Y., Ratner, A., Jacob, B., Huang, J., Williams, P. G., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1044 · Cited by 1,315 · see citing works
High-throughput generation, optimization and analysis of genome-scale metabolic models
Henry, C. S., DeJongh, M., Best, A. A., Frybarger, P. M., Linsay, B., & Stevens, R. L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1672 · Cited by 1,090 · see citing works
Genome-scale models of microbial cells: evaluating the consequences of constraints
Price, N. D., Reed, J. L., & Palsson, B. Ø. (2004) · Nature Reviews Microbiology · doi:10.1038/nrmicro1023 · Cited by 1,024 · see citing works
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
Reed, J. L., Vo, T. D., Schilling, C. H., & Palsson, B. Ø. (2003) · Genome biology · doi:10.1186/gb-2003-4-9-r54 · Cited by 1,001 · see citing works
Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use
Varma, A., & Palsson, B. Ø. (1994) · Nature Biotechnology · doi:10.1038/nbt1094-994 · Cited by 959 · see citing works
Reconstruction of biochemical networks in microorganisms
Feist, A. M., Herrgård, M. J., Thiele, I., Reed, J. L., & Palsson, B. Ø. (2008) · Nature Reviews Microbiology · doi:10.1038/nrmicro1949 · Cited by 859 · see citing works
Autotrophy at the thermodynamic limit of life: a model for energy conservation in acetogenic bacteria
Schuchmann, K., & Müller, V. (2014) · Nature Reviews Microbiology · doi:10.1038/nrmicro3365 · Cited by 845 · see citing works
Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
Lewis, N. E., Nagarajan, H., & Palsson, B. O. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2737 · Cited by 779 · see citing works
Genome Sequence and Comparative Analysis of the Solvent-Producing Bacterium Clostridium acetobutylicum
Nölling, J., Breton, G., Omelchenko, M. V., Makarova, K. S., Zeng, Q., Gibson, R., Lee, H. M., Dubois, J., Qiu, D., Hitti, J., et al. (2001) · Journal of Bacteriology · doi:10.1128/jb.183.16.4823-4838.2001 · Cited by 767 · see citing works
Alternative Pathways of Carbon Dioxide Fixation: Insights into the Early Evolution of Life?
Fuchs, G. (2011) · Annual Review of Microbiology · doi:10.1146/annurev-micro-090110-102801 · Cited by 726 · see citing works
Clostridium ljungdahlii represents a microbial production platform based on syngas
Köpke, M., Held, C., Hujer, S., Liesegang, H., Wiezer, A., Wollherr, A., Ehrenreich, A., Liebl, W., Gottschalk, G., & Dürre, P. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1004716107 · Cited by 660 · see citing works
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions
Schellenberger, J., Park, J. O., Conrad, T. M., & Palsson, B. Ø. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-213 · Cited by 585 · see citing works
Old Acetogens, New Light
Drake, H. L., Gößner, A. S., & Daniel, S. L. (2008) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1419.016 · Cited by 578 · see citing works
Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and Gene Essentiality Data
Oh, Y., Palsson, B. Ø., Park, S. M., Schilling, C. H., & Mahadevan, R. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m703759200 · Cited by 447 · see citing works
Enzymology of the Wood–Ljungdahl Pathway of Acetogenesis
Ragsdale, S. W. (2008) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1419.015 · Cited by 384 · see citing works
Energy conservation in Acetogenic Bacteria
Müller, V. (2003) · Applied and Environmental Microbiology · doi:10.1128/aem.69.11.6345-6353.2003 · Cited by 335 · see citing works
A New Type of Glucose Fermentation by Clostridium thermoaceticum
Fontaine, F. E., Peterson, W. H., McCoy, E., Johnson, M. J., & Ritter, G. J. (1942) · Journal of Bacteriology · doi:10.1128/jb.43.6.701-715.1942 · Cited by 295 · see citing works
Purification and properties of NADP-dependent formate dehydrogenase from Clostridium thermoaceticum, a tungsten–selenium–iron protein
Yamamoto, I., Saiki, T., Liu, S. M., & Ljungdahl, L. G. (1983) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)33062-x · Cited by 276 · see citing works
An Ancient Pathway Combining Carbon Dioxide Fixation with the Generation and Utilization of a Sodium Ion Gradient for ATP Synthesis
Poehlein, A., Schmidt, S., Kaster, A.-K., Goenrich, M., Vollmers, J., Thürmer, A., Bertsch, J., Schuchmann, K., Voigt, B., Hecker, M., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033439 · Cited by 274 · see citing works
The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum )
Pierce, E., Xie, G. G., Barabote, R. D., Saunders, E. H., Han, C. S., Detter, J. C., Richardson, P., Brettin, T. S., Das, A., Ljungdahl, L. G., et al. (2008) · Environmental Microbiology · doi:10.1111/j.1462-2920.2008.01679.x · Cited by 267 · see citing works
Chemiosmotic coupling in energy transduction: A logical development of biochemical knowledge
Mitchell, P. D. (1972) · Journal of Bioenergetics and Biomembranes · doi:10.1007/bf01515993 · Cited by 253 · see citing works
Stoichiometric and energetic analyses of non-photosynthetic CO2-fixation pathways to support synthetic biology strategies for production of fuels and chemicals
Fast, A. G., & Papoutsakis, E. T. (2012) · Current Opinion in Chemical Engineering · doi:10.1016/j.coche.2012.07.005 · Cited by 247 · see citing works
Metabolism of homoacetogens
Diekert, G. B., & Wohlfarth, G. (1994) · Antonie van Leeuwenhoek · doi:10.1007/bf00871640 · Cited by 226 · see citing works
Energy-Converting [NiFe] Hydrogenases from Archaea and Extremophiles: Ancestors of Complex I
Hedderich, R. (2004) · Journal of Bioenergetics and Biomembranes · doi:10.1023/b:jobb.0000019599.43969.33 · Cited by 222 · see citing works
Characterization of the H2- and CO-dependent chemolithotrophic potentials of the acetogens Clostridium thermoaceticum and Acetogenium kivui
Daniel, S. L., Hsu, T. D., Dean, S., & Drake, H. L. (1990) · Journal of Bacteriology · doi:10.1128/jb.172.8.4464-4471.1990 · Cited by 196 · see citing works
Physiology of the thermophilic acetogen Moorella thermoacetica
Drake, H. L., & Daniel, S. L. (2004) · Research in Microbiology · doi:10.1016/j.resmic.2004.10.002 · Cited by 194 · see citing works
Electron Bifurcation Involved in the Energy Metabolism of the Acetogenic Bacterium Moorella thermoacetica Growing on Glucose or H 2 plus CO 2
Huang, H., Wang, S., Moll, J., & Thauer, R. K. (2012) · Journal of Bacteriology · doi:10.1128/jb.00385-12 · Cited by 177 · see citing works
Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii
Nagarajan, H., Sahin, M., Nogales, J., Latif, H., Lovley, D. R., Ebrahim, A., & Zengler, K. (2013) · Microbial Cell Factories · doi:10.1186/1475-2859-12-118 · Cited by 170 · see citing works
Self-citation
Genome‐scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis
Senger, R. S., & Papoutsakis, E. T. (2008) · Biotechnology and Bioengineering · doi:10.1002/bit.22010 · Cited by 169 · see citing works
Fumarate respiration of Wolinella succinogenes: enzymology, energetics and coupling mechanism
Kröger, A., Biel, S., Simon, J., Groß, R., Unden, G., & Lancaster, C. R. D. (2002) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/s0005-2728(01)00234-1 · Cited by 159 · see citing works
Bacterial fumarate respiration
Kr�ger, A., Geisler, V., Lemma, E., Theis, F., & Lenger, R. (1992) · Archives of Microbiology · doi:10.1007/bf00245358 · Cited by 152 · see citing works
A Reversible Electron-Bifurcating Ferredoxin- and NAD-Dependent [FeFe]-Hydrogenase (HydABC) in Moorella thermoacetica
Wang, S., Huang, H., Kahnt, J., & Thauer, R. K. (2013) · Journal of Bacteriology · doi:10.1128/jb.02158-12 · Cited by 140 · see citing works
Carbon Dioxide Utilization in the Synthesis of Acetic Acid by Clostridium Thermoaceticum
Barker, H. A., & Kamen, M. D. (1945) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.31.8.219 · Cited by 123 · see citing works
Presence of Cytochrome and Menaquinone in Clostridium formicoaceticum and Clostridium thermoaceticum
Gottwald, M., Andreesen, J. R., LeGall, J., & Ljungdahl, L. G. (1975) · Journal of Bacteriology · doi:10.1128/jb.122.1.325-328.1975 · Cited by 118 · see citing works
Discovery of a Ferredoxin:NAD+‐Oxidoreductase (Rnf) in Acetobacterium woodii
Müller, V., Imkamp, F., Biegel, E., Schmidt, S., & Dilling, S. (2008) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1419.011 · Cited by 117 · see citing works
Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production
Roberts, S. B., Gowen, C. M., Brooks, J. P., & Fong, S. S. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-31 · Cited by 114 · see citing works
Genome‐scale metabolic modeling of a clostridial co‐culture for consolidated bioprocessing
Salimi, F., Zhuang, K. H., & Mahadevan, R. (2010) · Biotechnology Journal · doi:10.1002/biot.201000159 · Cited by 113 · see citing works
Evidence for a Hexaheteromeric Methylenetetrahydrofolate Reductase in Moorella thermoacetica
Mock, J., Wang, S., Huang, H., Kahnt, J., & Thauer, R. K. (2014) · Journal of Bacteriology · doi:10.1128/jb.01839-14 · Cited by 99 · see citing works
Structure and function of a menaquinone involved in electron transport in membranes of Clostridium thermoautotrophicum and Clostridium thermoaceticum
Das, A., Hugenholtz, J., van HALBEEK, H., & Ljungdahl, L. G. (1989) · Journal of Bacteriology · doi:10.1128/jb.171.11.5823-5829.1989 · Cited by 79 · see citing works
Acetogenesis
Drake, H. L. (1994) · Springer eBooks · doi:10.1007/978-1-4615-1777-1 · Cited by 74 · see citing works
A Life with Acetogens, Thermophiles, and Cellulolytic Anaerobes
Ljungdahl, L. G. (2009) · Annual Review of Microbiology · doi:10.1146/annurev.micro.091208.073617 · Cited by 73 · see citing works
Properties of Nicotinamide Adenine Dinucleotide Phosphate-Dependent Formate Dehydrogenase from Clostridium thermoaceticum
Li, L.-F., Ljungdahl, L. G., & Wood, H. G. (1966) · Journal of Bacteriology · doi:10.1128/jb.92.2.405-412.1966 · Cited by 63 · see citing works
Corrinoids in anaerobic bacteria
Stupperich, E., EISINGER, H. J., & Schurr, S. (1990) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1990.tb04936.x · Cited by 60 · see citing works
Brock Biology of Microorganisms (9th edn). Michael E. Madigan, John M. Martinko, Jack Parker
Guerrero, R. (2000) · International Microbiology · doi:10.2436/im.v3i2.9260 · Cited by 48 · see citing works
Isoprenoid quinone, cellular fatty acid composition and diaminopimelic acid isomers of newly classified thermophilic anaerobic Gram-positive bacteria
Yamamoto, K., Murakami, R., & Takamura, Y. (1998) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1998.tb12968.x · Cited by 29 · see citing works

Flagged first, then by citations

1 of the 58 references couldn’t be matched to a known paper.

Sorted by citations

Gas Fermentation—A Flexible Platform for Commercial Scale Production of Low-Carbon-Fuels and Chemicals from Waste and Renewable Feedstocks
Liew, F., Martin, M. E., Tappel, R. C., Heijstra, B. D., Mihalcea, C., & Köpke, M. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00694 · Cited by 485 · see citing works
Autocatalytic chemical networks at the origin of metabolism
Xavier, J. C., Hordijk, W., Kauffman, S., Steel, M., & Martin, W. F. (2020) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2019.2377 · Cited by 196 · see citing works
Genome-Scale Metabolic Modeling Enables In-Depth Understanding of Big Data
Passi, A., Tibocha‐Bonilla, J. D., Kumar, M., Tec-Campos, D., Zengler, K., & Zúñiga, C. (2021) · Metabolites · doi:10.3390/metabo12010014 · Cited by 169 · see citing works
Maintenance of ATP Homeostasis Triggers Metabolic Shifts in Gas-Fermenting Acetogens
Valgepea, K., Lemgruber, R. D. S. P., Meaghan, K., Palfreyman, R. W., Abdalla, T., Heijstra, B. D., Behrendorff, J. B. Y. H., Tappel, R. C., Köpke, M., Simpson, S. D., et al. (2017) · Cell Systems · doi:10.1016/j.cels.2017.04.008 · Cited by 162 · see citing works
Bacterial Anaerobic Synthesis Gas (Syngas) and CO 2 + H 2 Fermentation
Bengelsdorf, F. R., Beck, M. H., Erz, C., Hoffmeister, S., Karl, M. M., Riegler, P., Wirth, S., Poehlein, A., Weuster‐Botz, D., & Dürre, P. (2018) · Advances in applied microbiology · doi:10.1016/bs.aambs.2018.01.002 · Cited by 164 · see citing works
Biochemical Production and Separation of Carboxylic Acids for Biorefinery Applications
Murali, N., Srinivas, K., & Ahring, B. K. (2017) · Fermentation · doi:10.3390/fermentation3020022 · Cited by 126 · see citing works
Synergistic substrate cofeeding stimulates reductive metabolism
Park, J. O., Liu, N., Holinski, K. M., Emerson, D. F., Qiao, K., Woolston, B. M., Xu, J., Lazar, Z., Islam, M. A., Vidoudez, C., et al. (2019) · Nature Metabolism · doi:10.1038/s42255-019-0077-0 · Cited by 115 · see citing works
Valorization of C1 gases to value-added chemicals using acetogenic biocatalysts
Bae, J., Song, Y., Lee, H., Shin, J., Jin, S., Kang, S., & Cho, B. (2021) · Chemical Engineering Journal · doi:10.1016/j.cej.2021.131325 · Cited by 93 · see citing works
Advances in systems metabolic engineering of autotrophic carbon oxide-fixing biocatalysts towards a circular economy
Pavan, M., Reinmets, K., Garg, S., Mueller, A. P., Marcellin, E., Köpke, M., & Valgepea, K. (2022) · Metabolic Engineering · doi:10.1016/j.ymben.2022.01.015 · Cited by 88 · see citing works
Gas fermentation: cellular engineering possibilities and scale up
Heijstra, B. D., Leang, C., & Juminaga, A. (2017) · Microbial Cell Factories · doi:10.1186/s12934-017-0676-y · Cited by 92 · see citing works
Systems-level engineering and characterisation of Clostridium autoethanogenum through heterologous production of poly-3-hydroxybutyrate (PHB)
Lemgruber, R. D. S. P., Valgepea, K., Tappel, R. C., Behrendorff, J. B. Y. H., Palfreyman, R. W., Plan, M. R., Hodson, M. P., Simpson, S. D., Nielsen, L. K., Köpke, M., et al. (2019) · Metabolic Engineering · doi:10.1016/j.ymben.2019.01.003 · Cited by 83 · see citing works
Overcoming the energetic limitations of syngas fermentation
Molitor, B., Marcellin, E., & Angenent, L. T. (2017) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2017.10.003 · Cited by 71 · see citing works
Genetic and metabolic engineering challenges of C1-gas fermenting acetogenic chassis organisms
Bourgade, B., Minton, N. P., & Islam, M. A. (2021) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuab008 · Cited by 66 · see citing works
Towards continuous industrial bioprocessing with solventogenic and acetogenic clostridia: challenges, progress and perspectives
Vees, C. A., Neuendorf, C. S., & Pflügl, S. (2020) · Journal of Industrial Microbiology & Biotechnology · doi:10.1007/s10295-020-02296-2 · Cited by 65 · see citing works
Analysis of the Core Genome and Pan-Genome of Autotrophic Acetogenic Bacteria
Shin, J., Song, Y., Jeong, Y., & Cho, B. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01531 · Cited by 64 · see citing works
Critical factors affecting the integration of biomass gasification and syngas fermentation technology
Ramachandriya, K. D., Kundiyana, D. K., Sharma, A. M., Kumar, A., V, Atiyeh, H. K., Huhnke, R. L., & Wilkins, M. R. (2016) · AIMS bioengineering · doi:10.3934/bioeng.2016.2.188 · Cited by 60 · see citing works
Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen
Liu, J. K., Lloyd, C. J., Al‐Bassam, M. M., Ebrahim, A., Kim, J.-N., Olson, C. A., Aksenov, A. A., Dorrestein, P. C., & Zengler, K. (2019) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006848 · Cited by 59 · see citing works
Thermodynamics and economic feasibility of acetone production from syngas using the thermophilic production host Moorella thermoacetica
Redl, S., Sukumara, S., Ploeger, T., Wu, L., Jensen, T. Ø., Nielsen, A. T., & Noorman, H. J. (2017) · Biotechnology for Biofuels · doi:10.1186/s13068-017-0827-8 · Cited by 43 · see citing works
Embracing a low-carbon future by the production and marketing of C1 gas protein
Xu, J., Wang, J., Ma, C., Wei, Z., Zhai, Y., Tian, N., Zhu, Z., Xue, M., & Li, D. (2023) · Biotechnology Advances · doi:10.1016/j.biotechadv.2023.108096 · Cited by 41 · see citing works
Impact of Nitrogen-Containing Compounds on Secondary Metabolism in Streptomyces spp.—A Source of Metabolic Engineering Strategies
Krysenko, S. (2023) · SynBio · doi:10.3390/synbio1030015 · Cited by 38 · see citing works
Experimental testing of a spatiotemporal metabolic model for carbon monoxide fermentation with Clostridium autoethanogenum
Chen, J., Daniell, J., Griffin, D. W., Li, X., & Henson, M. A. (2017) · Biochemical Engineering Journal · doi:10.1016/j.bej.2017.10.018 · Cited by 37 · see citing works
Moorella thermoacetica: A promising cytochrome- and quinone-containing acetogenic bacterium as platform for a CO2-based bioeconomy
Rosenbaum, F. P., & Müller, V. (2023) · Green Carbon · doi:10.1016/j.greenca.2023.06.002 · Cited by 29 · see citing works
Exploring biochemical pathways for mono-ethylene glycol (MEG) synthesis from synthesis gas
Islam, M. A., Hadadi, N., Ataman, M., Vassily Hatzimanikatis, A., & Stephanopoulos, G. N. (2017) · Metabolic Engineering · doi:10.1016/j.ymben.2017.04.005 · Cited by 29 · see citing works
Low-Carbon Fuel and Chemical Production by Anaerobic Gas Fermentation
Daniell, J., Nagaraju, S., Burton, F., Köpke, M., & Simpson, S. D. (2015) · Advances in biochemical engineering, biotechnology · doi:10.1007/10_2015_5005 · Cited by 28 · see citing works
Analytical tools for unravelling the metabolism of gas-fermenting Clostridia
Heffernan, J. K., Mahamkali, V., Valgepea, K., Marcellin, E., & Nielsen, L. K. (2022) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2022.102700 · Cited by 24 · see citing works
Basics of genome-scale metabolic modeling and applications on C1-utilization
Kabimoldayev, I., Nguyen, A. D., Yang, L., Park, S., Lee, E. Y., & Kim, D. (2018) · FEMS Microbiology Letters · doi:10.1093/femsle/fny241 · Cited by 18 · see citing works
Thermophilic Moorella thermoacetica as a platform microorganism for C1 gas utilization: physiology, engineering, and applications
Jia, D., Deng, W., Hu, P., Jiang, W., & Gu, Y. (2023) · Bioresources and Bioprocessing · doi:10.1186/s40643-023-00682-z · Cited by 14 · see citing works
Ethanol yield and sugar usability in thermophilic ethanol production from lignocellulose hydrolysate by genetically engineered Moorella thermoacetica
Rahayu, F., Tajima, T., Kato, J., Kato, S., & Nakashimada, Y. (2019) · Journal of Bioscience and Bioengineering · doi:10.1016/j.jbiosc.2019.08.008 · Cited by 14 · see citing works
Genome‐scale metabolic modelling of extremophiles and its applications in astrobiological environments
Noirungsee, N., Changkhong, S., Phinyo, K., Suwannajak, C., Tanakul, N., & Inwongwan, S. (2024) · Environmental Microbiology Reports · doi:10.1111/1758-2229.13231 · Cited by 9 · see citing works
Autocatalytic chemical networks preceded proteins and RNA in evolution
Xavier, J. C., Hordijk, W., Kauffman, S., Steel, M., & Martin, W. F. (2019) · doi:10.1101/693879 · Cited by 8 · see citing works
Impact of Silver and Copper Oxide Nanoparticles on Anaerobic Digestion of Sludge and Bacterial Community Structure
Abdulsada, Z. S., Kibbee, R. J., Princz, J., & Örmeci, B. (2025) · Nanomaterials · doi:10.3390/nano15030236 · Cited by 8 · see citing works
Reversible Hydrogenase Activity Confers Flexibility to Balance Intracellular Redox in Moorella thermoacetica
Kobayashi, S., Kato, J., Wada, K., Takemura, K., Kato, S., Fujii, T., Iwasaki, Y., Aoi, Y., Morita, T., Matsushika, A., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.897066 · Cited by 8 · see citing works
Genome-Scale Modeling of Thermophilic Microorganisms
Dahal, S., Poudel, S., & Thompson, R. A. (2016) · Advances in biochemical engineering, biotechnology · doi:10.1007/10_2016_45 · Cited by 8 · see citing works
Utilization of the liquid one carbon feedstocks methanol and formate for acetogenic bioproduction of chemicals and fuels
Pettinato, E., Hocq, R., & Pflügl, S. (2025) · Bioresource Technology · doi:10.1016/j.biortech.2025.132643 · Cited by 7 · see citing works
Systems Biology on Acetogenic Bacteria for Utilizing C1 Feedstocks
Song, Y., Bae, J., Shin, J., Jin, S., Kang, S., Lee, H., Cho, S., & Cho, B. (2022) · Advances in biochemical engineering, biotechnology · doi:10.1007/10_2021_199 · Cited by 5 · see citing works
Engineering alternative bacterial platforms for sustainable bioproduction
Cabas, M. B., & Billerbeck, S. (2026) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2026.102720 · Cited by 1 · see citing works
Recent advances on bio-alcohol production from syngas using microorganisms
Woo, J. E., & Jang, Y. (2017) · Journal of Applied Biological Chemistry · doi:10.3839/jabc.2017.052
Transformation and Effects of Silver and Copper Oxide Nanoparticles during Treatment and after Land Application of Sludge
Abdulsada, Z. S. (2019) · doi:10.22215/etd/2019-13939
Carboxylic Acid Production
Lidén, G. (2017) · MDPI eBooks · doi:10.3390/books978-3-03842-553-3
Reconstructing and analyzing the experimentally-supported binary protein-protein interaction network of Moorella thermoacetica, an anaerobe of industrial interest
Savvopoulou, V. A., & Klapa, M. I. (2024) · IFAC-PapersOnLine · doi:10.1016/j.ifacol.2024.10.009
Thermodynamic metabolic modeling of growth and bioproduction potential of the acetogen Acetobacterium woodii with and without redox cofactor swaps
Bauer, J., von Kamp, A., Pflügl, S., & Klamt, S. (2026) · Synthetic and Systems Biotechnology · doi:10.1016/j.synbio.2026.05.007

Physiology of the thermophilic acetogen Moorella thermoacetica
Drake, H. L., & Daniel, S. L. (2004) · Research in Microbiology · doi:10.1016/j.resmic.2004.03.003 · Cited by 57 · see citing works
Complete Genome Sequence of the Type Strain of the Acetogenic Bacterium Moorella thermoacetica DSM 521 T
Poehlein, A., Bengelsdorf, F. R., Esser, C., Schiel‐Bengelsdorf, B., Daniel, R., & Dürre, P. (2015) · Genome Announcements · doi:10.1128/genomea.01159-15 · Cited by 23 · see citing works
Additional file 1 of Metabolic engineering of Moorella thermoacetica for thermophilic bioconversion of gaseous substrates to a volatile chemical
Kato, J., Takemura, K., Kato, S., Fujii, T., Wada, K., Iwasaki, Y., Aoi, Y., Matsushika, A., Murakami, K., & Nakashimada, Y. (2021) · Figshare · doi:10.6084/m9.figshare.14478669
The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum )
Pierce, E., Xie, G. G., Barabote, R. D., Saunders, E. H., Han, C. S., Detter, J. C., Richardson, P., Brettin, T. S., Das, A., Ljungdahl, L. G., et al. (2008) · Environmental Microbiology · doi:10.1111/j.1462-2920.2008.01679.x · Cited by 267 · see citing works
Ensemble cell-wide kinetic modeling of anaerobic organisms to support fuels and chemicals production
Dash, S., (3995480), A. K., (4116055), A. I., (2176086), Y. Z., (345366), P. L., (7333295), J. C. L., Stephanopoulos, G. N., & (7333298), C. D. M. (2019) · Loughborough University Research Repository (Loughborough University)

Authors: Islam, M. A., Zengler, K., Edwards, E. A., Mahadevan, R., & Stephanopoulos, G.
Affiliations: Massachusetts Institute of Technology (US)
University of California San Diego (US)
University of Toronto (CA)
Corresponding author: Mahadevan, Radhakrishnan
Stephanopoulos, Gregory
ORCID: Islam, M. Ahsanul
Zengler, Karsten
Edwards, Elizabeth A.
Mahadevan, Radhakrishnan
Stephanopoulos, Gregory
Venue: Integrative Biology
Publisher: Oxford University Press (OUP)
Published: 2015
Volume: 7
Issue: 8
Pages: 869-882
ISSN: 1757-9694 (ISSN-L)
1757-9708
DOI: 10.1039/c5ib00095e
OpenAlex: W1920412431
Semantic Scholar: 13594a852785fd4f83f62b09af6016f903bdda7e
Cited by: 41
References: 58
Citations by year: 2026: 2 · 2025: 2 · 2024: 2 · 2023: 4 · 2022: 4 · 2021: 3 · 2020: 2 · 2019: 6 · 2018: 2 · 2017: 9 · 2016: 4 · 2015: 1
FWCI: 2.31
Type: journal article
Language: en
Open access: green
dspace.lboro.ac.uk
Licence: cc-by-nc-nd
Locations: Integrative Biology (publishedVersion)
PubMed (publishedVersion)
Loughborough University Institutional Repository (Loughborough University) (submittedVersion, cc-by-nc-nd)
Funders: U.S. Department of Energy
University of California, San Diego
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords: Moorella thermoacetica, genome-scale metabolic models, acetogenesis, homoacetogenesis, syngas conversion, acetyl-CoA biosynthesis, anaerobic metabolism, metabolic network reconstruction, metabolic engineering, industrial biotechnology
MeSH terms: Bacterial Proteins, Computer Simulation, Models, Biological, Signal Transduction, Genome, Bacterial, Proteome, Metabolic Networks and Pathways, Metabolome, Moorella

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model

Abstract

Integrity signals

Claims the paper makes

Claims other papers make about this one

Cites

Cited by

Related

Record

About these checks