Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii

Nagarajan, Harish; Sahin, Merve; Nogales, Juan; Latif, Haythem; Lovley, Derek R; Ebrahim, Ali; Zengler, Karsten

doi:10.1186/1475-2859-12-118

Cited by 172Microbial Metabolic Engineering and BioproductionBiofuel production and bioconversionGene Regulatory Network Analysis

Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii

Open access

Nagarajan, Harish, Sahin, Merve, Nogales, Juan, Latif, Haythem, Lovley, Derek R, Ebrahim, Ali, Zengler, Karsten·2013·Microbial Cell Factories

DOI 10.1186/1475-2859-12-118PMC PMC4222884

Open this paper in CoChat — free account Open PDF

Abstract

BACKGROUND: The metabolic capabilities of acetogens to ferment a wide range of sugars, to grow autotrophically on H2/CO2, and more importantly on synthesis gas (H2/CO/CO2) make them very attractive candidates as production hosts for biofuels and biocommodities. Acetogenic metabolism is considered one of the earliest modes of bacterial metabolism. A thorough understanding of various factors governing the metabolism, in particular energy conservation mechanisms, is critical for metabolic engineering of acetogens for targeted production of desired chemicals. RESULTS: Here, we present the genome-scale metabolic network of Clostridium ljungdahlii, the first such model for an acetogen. This genome-scale model (iHN637) consisting of 637 genes, 785 reactions, and 698 metabolites captures all the major central metabolic and biosynthetic pathways, in particular pathways involved in carbon fixation and energy conservation. A combination of metabolic modeling, with physiological and transcriptomic data provided insights into autotrophic metabolism as well as aided the characterization of a nitrate reduction pathway in C. ljungdahlii. Analysis of the iHN637 metabolic model revealed that flavin based electron bifurcation played a key role in energy conservation during autotrophic growth and helped identify genes for some of the critical steps in this mechanism. CONCLUSIONS: iHN637 represents a predictive model that recapitulates experimental data, and provides valuable insights into the metabolic response of C. ljungdahlii to genetic perturbations under various growth conditions. Thus, the model will be instrumental in guiding metabolic engineering of C. ljungdahlii for the industrial production of biocommodities and biofuels.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1186/1475-2859-12-118

Cites

52 of 52 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

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 Nagarajan et al., 2013
Transcriptomics analyses have been performed for C. autoethanogenum and C. ljungdahlii.
“and transcriptomics analyses of C. autoethanogenum (Mock et al., 2015; Marcellin et al., 2016) and C. ljungdahlii (Nagarajan et al., 2013; Tan et al., 2013; Whitham 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 Nagarajan et al., 2013

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

KEGG: Kyoto Encyclopedia of Genes and Genomes
Kanehisa, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.27 · Cited by 37,077 · see citing works
KEGG: Kyoto Encyclopedia of Genes and Genomes
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232 · see citing works
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849 · see citing works
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556 · 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
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 genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic information
Feist, A. M., Henry, C. S., Reed, J. L., Krummenacker, M., Joyce, A. R., Karp, P. D., Broadbelt, L. J., Vassily Hatzimanikatis, A., & Palsson, B. Ø. (2007) · Molecular Systems Biology · doi:10.1038/msb4100155 · Cited by 1,367 · 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
Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol
Yim, H. H., Haselbeck, R. J., Niu, W., Pujol-Baxley, C., Burgard, A. P., Boldt, J., Khandurina, J., Trawick, J. D., Osterhout, R. E., Stephen, R., et al. (2011) · Nature Chemical Biology · doi:10.1038/nchembio.580 · Cited by 1,119 · 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
Microbial Electrosynthesis: Feeding Microbes Electricity To Convert Carbon Dioxide and Water to Multicarbon Extracellular Organic Compounds
Nevin, K. P., Woodard, T. L., Franks, A. E., Summers, Z. M., & Lovley, D. R. (2010) · mBio · doi:10.1128/mbio.00103-10 · Cited by 1,068 · see citing works
Self-citation
Transcriptome analysis by strand-specific sequencing of complementary DNA
Parkhomchuk, D., Borodina, T. A., Amstislavskiy, V. S., Banaru, M., Hallen, L., Krobitsch, S., Lehrach, H. R., & Солдатов, А. В. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp596 · Cited by 934 · see citing works
Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation
Buckel, W., & Thauer, R. K. (2013) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/j.bbabio.2012.07.002 · Cited by 797 · 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
Self-citation
Electrosynthesis of Organic Compounds from Carbon Dioxide Is Catalyzed by a Diversity of Acetogenic Microorganisms
Nevin, K. P., Hensley, S. A., Franks, A. E., Summers, Z. M., Ou, J., Woodard, T. L., Snoeyenbos-West, O., & Lovley, D. R. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.02642-10 · Cited by 722 · see citing works
Self-citation
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
The biomass objective function
Feist, A. M., & Palsson, B. Ø. (2010) · Current Opinion in Microbiology · doi:10.1016/j.mib.2010.03.003 · Cited by 608 · 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
The Autotrophic Pathway of Acetate Synthesis in Acetogenic Bacteria
Ljungdhal, L. G. (1986) · Annual Review of Microbiology · doi:10.1146/annurev.mi.40.100186.002215 · Cited by 575 · see citing works
High-Throughput Illumina Strand-Specific RNA Sequencing Library PreparationPreprint
Zhong, S., Joung, J., Zheng, Y., Chen, Y.-R., Liu, B., Shao, Y., Xiang, J., Fei, Z., & Giovannoni, J. J. (2011) · Cold Spring Harbor Protocols · doi:10.1101/pdb.prot5652 · Cited by 471 · 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
2,3-Butanediol Production by Acetogenic Bacteria, an Alternative Route to Chemical Synthesis, Using Industrial Waste Gas
Köpke, M., Mihalcea, C., Liew, F. E., Tizard, J. H., Ali, M., Conolly, J. J., Al‐Sinawi, B., & Simpson, S. D. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.00355-11 · Cited by 418 · see citing works
Nitrate reduction by shaking with cadmiumAlternative to cadmium columns
JONES, M. (1984) · Water Research · doi:10.1016/0043-1354(84)90215-x · Cited by 380 · see citing works
Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli
McCloskey, D., Palsson, B. Ø., & Feist, A. M. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.18 · Cited by 320 · see citing works
Clostridium ljungdahlii sp. nov., an Acetogenic Species in Clostridial rRNA Homology Group I
Tanner, R. S., Miller, L. M., & Yang, D. (1993) · International Journal of Systematic Bacteriology · doi:10.1099/00207713-43-2-232 · Cited by 303 · see citing works
Systems approach to refining genome annotation
Reed, J. L., Patel, T., Chen, K. H., Joyce, A. R., Applebee, M. K., Herring, C. D., Bui, O., Knight, E. M., Fong, S. S., & Palsson, B. Ø. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603364103 · Cited by 283 · see citing works
The wall teichoic acid and lipoteichoic acid polymers of Staphylococcus aureus
Xia, G., Kohler, T. P., & Peschel, A. (2009) · International Journal of Medical Microbiology · doi:10.1016/j.ijmm.2009.10.001 · Cited by 279 · 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
Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901
Wu, M., Ren, Q., Durkin, A. S., Daugherty, S. C., Brinkac, L. M., Dodson, R. J., Madupu, R., Sullivan, S. A., Kolonay, J. F., Nelson, W. C., et al. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010065 · Cited by 261 · see citing works
NADP-Specific Electron-Bifurcating [FeFe]-Hydrogenase in a Functional Complex with Formate Dehydrogenase in Clostridium autoethanogenum Grown on CO
Wang, S., Huang, H., Kahnt, J., Mueller, A. P., Köpke, M., & Thauer, R. K. (2013) · Journal of Bacteriology · doi:10.1128/jb.00678-13 · Cited by 237 · see citing works
NADP + Reduction with Reduced Ferredoxin and NADP + Reduction with NADH Are Coupled via an Electron-Bifurcating Enzyme Complex in Clostridium kluyveri
Wang, S., Huang, H., Moll, J., & Thauer, R. K. (2010) · Journal of Bacteriology · doi:10.1128/jb.00612-10 · Cited by 230 · see citing works
A Bacterial Electron-bifurcating Hydrogenase
Schuchmann, K., & Müller, V. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.395038 · Cited by 218 · see citing works
The Rnf Complex of Clostridium ljungdahlii Is a Proton-Translocating Ferredoxin:NAD + Oxidoreductase Essential for Autotrophic Growth
Tremblay, P., Zhang, T., Dar, S. A., Leang, C., & Lovley, D. R. (2012) · mBio · doi:10.1128/mbio.00406-12 · Cited by 208 · see citing works
Self-citation
A genetic system for Clostridium ljungdahlii: a chassis for autotrophic production of biocommodities and a model homoacetogen
Leang, C., Ueki, T., Nevin, K. P., & Lovley, D. R. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.02891-12 · Cited by 202 · see citing works
Self-citation
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
Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network
Lee, J., Yun, H., Feist, A. M., Palsson, B. Ø., & Lee, S. Y. (2008) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-008-1654-4 · Cited by 173 · see citing works
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
Systematizing the generation of missing metabolic knowledge
Orth, J. D., & Palsson, B. Ø. (2010) · Biotechnology and Bioengineering · doi:10.1002/bit.22844 · Cited by 155 · see citing works
Adaptations to Submarine Hydrothermal Environments Exemplified by the Genome of Nautilia profundicola
Campbell, B. J., Smith, J. L., Hanson, T. E., Klotz, M. G., Stein, L. Y., Lee, C. K., Wu, D., Robinson, J. M., Khouri, H. M., Eisen, J. A., et al. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000362 · Cited by 143 · see citing works
Sulfide-Driven Microbial Electrosynthesis
Gong, Y., Ebrahim, A., Feist, A. M., Embree, M., Zhang, T., Lovley, D. R., & Zengler, K. (2012) · Environmental Science & Technology · doi:10.1021/es303837j · Cited by 117 · see citing works
Self-citation
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
The Physiological Function of Nitrate Reduction in Clostridium perfringens
HASAN, S. M., & Hall, J. B. (1975) · Journal of General Microbiology · doi:10.1099/00221287-87-1-120 · Cited by 112 · see citing works
Hydrogen, metals, bifurcating electrons, and proton gradients: The early evolution of biological energy conservation
Martin, W. F. (2012) · FEBS Letters · doi:10.1016/j.febslet.2011.09.031 · Cited by 108 · see citing works
Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052
Milne, C. B., Eddy, J. A., Raju, R., Ardekani, S., Kim, P., Senger, R. S., Jin, Y., Blaschek, H. P., & Price, N. D. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-130 · Cited by 108 · see citing works
A flow injection-fluorometric method for the determination of ammonium in fresh and saline waters with a view to in situ analyses
Aminot, A. (2001) · Water Research · doi:10.1016/s0043-1354(00)00429-2 · Cited by 82 · see citing works
Aerobic Fermentation of d -Glucose by an Evolved Cytochrome Oxidase-Deficient Escherichia coli Strain
Portnoy, V. A., Herrgård, M. J., & Palsson, B. Ø. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.00880-08 · Cited by 68 · see citing works
RNA-seq-based comparative transcriptome analysis of the syngas-utilizing bacterium Clostridium ljungdahlii DSM 13528 grown autotrophically and heterotrophically
Tan, Y., Liu, J., Chen, X., Zheng, H., & Li, F. (2013) · Molecular BioSystems · doi:10.1039/c3mb70232d · Cited by 56 · see citing works
Does acetogenesis really require especially low reduction potential?
Bar‐Even, A. (2012) · Biochimica et Biophysica Acta (BBA) - Bioenergetics · doi:10.1016/j.bbabio.2012.10.007 · Cited by 42 · see citing works
Tight Coupling of Partial Reactions in the Acetyl-CoA Decarbonylase/Synthase (ACDS) Multienzyme Complex from Methanosarcina thermophila
Gencic, S., Duin, E. C., & Grahame, D. A. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.080994 · Cited by 40 · see citing works
Crystal ball – 2013
Curtis, T., Daran, J., Pronk, J., Frey, J., Jansson, J., Robbins-Pianka, A., Knight, R., Schnürer, A., Smets, B., Smid, E., et al. (2012) · Microbial Biotechnology · doi:10.1111/1751-7915.12014 · Cited by 12 · see citing works
Self-citation
Correction: Life in Hot Carbon Monoxide: The Complete Genome Sequence of Carboxydothermus hydrogenoformans Z-2901
Wu, M., Ren, Q., Durkin, A. S., Daugherty, S. C., Brinkac, L. M., Dodson, R. J., Madupu, R., Sullivan, S. A., Kolonay, J. F., Haft, D. H., et al. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020060 · Cited by 10 · see citing works
The future of sustainable fish production lies in vaccine research and development and revised regulatory measures
Curtis, T., Daran, J.-M. G., Pronk, J. T., Frey, J., Jansson, J. K., Robbins‐Pianka, A., Knight, R. D., Schnürer, A., Smets, B. F., Smid, E. J., et al. (2012) · doi:10.7892/boris.57862 · Cited by 6 · see citing works
Self-citation

Flagged first, then by citations

Sorted by citations

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
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
Supplementation of Saturated Long-Chain Fatty Acids Maintains Intestinal Eubiosis and Reduces Ethanol-induced Liver Injury in Mice
Chen, P., Torralba, M., Tan, J., Embree, M., Zengler, K., Stärkel, P., van Pijkeren, J.-P., DePew, J., Loomba, R., Ho, S. B., et al. (2015) · Gastroenterology · doi:10.1053/j.gastro.2014.09.014 · Cited by 322 · see citing works
Self-citation
C1-carbon sources for chemical and fuel production by microbial gas fermentation
Dürre, P., & Eikmanns, B. J. (2015) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2015.03.008 · Cited by 242 · see citing works
Metabolic engineering of Clostridium autoethanogenum for selective alcohol production
Liew, F. E., Henstra, A. M., Köpke, M., Winzer, K., Simpson, S. D., & Minton, N. P. (2017) · Metabolic Engineering · doi:10.1016/j.ymben.2017.01.007 · Cited by 239 · see citing works
Electroactive bacteria—molecular mechanisms and genetic tools
Sydow, A., Krieg, T. M., Mayer, F., Schrader, J., & Holtmann, D. (2014) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-014-6005-z · Cited by 238 · see citing works
Energy Conservation Associated with Ethanol Formation from H 2 and CO 2 in Clostridium autoethanogenum Involving Electron Bifurcation
Mock, J., Zheng, Y., Mueller, A. P., Ly, S., Tran, L., Segovia, S., Nagaraju, S., Köpke, M., Dürre, P., & Thauer, R. K. (2015) · Journal of Bacteriology · doi:10.1128/jb.00399-15 · Cited by 220 · see citing works
Trash to treasure: production of biofuels and commodity chemicals via syngas fermenting microorganisms
Latif, H., Zeidan, A. A., Nielsen, A. T., & Zengler, K. (2014) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2013.12.001 · Cited by 199 · see citing works
Self-citation
CO2 fixation by anaerobic non-photosynthetic mixotrophy for improved carbon conversion
Jones, S. W., Fast, A. G., Carlson, E. D., Wiedel, C. A., Au, J., Antoniewicz, M. R., Papoutsakis, E. T., & Tracy, B. P. (2016) · Nature Communications · doi:10.1038/ncomms12800 · Cited by 192 · see citing works
Converting carbon dioxide to butyrate with an engineered strain of Clostridium ljungdahlii
Ueki, T., Nevin, K. P., Woodard, T. L., & Lovley, D. R. (2014) · mBio · doi:10.1128/mbio.01636-14 · Cited by 175 · see citing works
Self-citation
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
Self-citation
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
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
Low carbon fuels and commodity chemicals from waste gases – systematic approach to understand energy metabolism in a model acetogen
Marcellin, E., Behrendorff, J. B., Nagaraju, S., DeTissera, S., Segovia, S., Palfreyman, R. W., Daniell, J., Licona-Cassani, C., Quek, L.-E., Speight, R., et al. (2016) · Green Chemistry · doi:10.1039/c5gc02708j · Cited by 159 · see citing works
Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models
Aite, M., Chevallier, M., Frioux, C., Trottier, C., Got, J., Cortés, M. P., Mendoza, S. N., Carrier, G., Dameron, O., Guillaudeux, N., et al. (2018) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1006146 · Cited by 137 · see citing works
H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum
Valgepea, K., Lemgruber, R. D. S. P., Abdalla, T., Binos, S., Takemori, N., Takemori, A., Tanaka, Y., Tappel, R. C., Köpke, M., Simpson, S. D., et al. (2018) · Biotechnology for Biofuels · doi:10.1186/s13068-018-1052-9 · Cited by 130 · see citing works
Metabolic engineering of Clostridium cellulolyticum for the production of n-butanol from crystalline cellulose
Gaida, S. M., Liedtke, A., Jentges, A. H. W., Engels, B., & Jennewein, S. (2016) · Microbial Cell Factories · doi:10.1186/s12934-015-0406-2 · Cited by 125 · see citing works
Overcoming Energetic Barriers in Acetogenic C1 Conversion
Katsyv, A., & Müller, V. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.621166 · Cited by 125 · see citing works
Arginine deiminase pathway provides ATP and boosts growth of the gas-fermenting acetogen Clostridium autoethanogenum
Valgepea, K., Loi, Q. K., Behrendorff, J. B. Y. H., Lemgruber, R. D. S. P., Plan, M. R., Hodson, M. P., Köpke, M., Nielsen, L. K., & Marcellin, E. (2017) · Metabolic Engineering · doi:10.1016/j.ymben.2017.04.007 · Cited by 118 · see citing works
Acetogenic mixotrophy: novel options for yield improvement in biofuels and biochemicals production
Fast, A. G., Schmidt, E. D., Jones, S. W., & Tracy, B. P. (2014) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2014.11.014 · Cited by 117 · see citing works
Microbial synthesis gas utilization and ways to resolve kinetic and mass-transfer limitations
Yasin, M., Jeong, Y., Park, S., Jeong, J., Lee, E. Y., Lovitt, R. W., Kim, B. H., Lee, J., & Chang, I. S. (2014) · Bioresource Technology · doi:10.1016/j.biortech.2014.11.022 · Cited by 111 · see citing works
A thermochemical–biochemical hybrid processing of lignocellulosic biomass for producing fuels and chemicals
Shen, Y., Jarboe, L. R., Brown, R. C., & Wen, Z. (2015) · Biotechnology Advances · doi:10.1016/j.biotechadv.2015.10.006 · Cited by 110 · see citing works
Rediverting carbon flux in Clostridium ljungdahlii using CRISPR interference (CRISPRi)
Woolston, B. M., Emerson, D. F., Currie, D. H., & Stephanopoulos, G. N. (2018) · Metabolic Engineering · doi:10.1016/j.ymben.2018.06.006 · Cited by 105 · see citing works
Engineering Clostridium for improved solvent production: recent progress and perspective
Cheng, C., Bao, T., & Yang, S. (2019) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-019-09916-7 · Cited by 95 · see citing works
Metabolic engineering in chemolithoautotrophic hosts for the production of fuels and chemicals
Nybo, S. E., Khan, N. E., Woolston, B. M., & Curtis, W. R. (2015) · Metabolic Engineering · doi:10.1016/j.ymben.2015.04.008 · Cited by 94 · 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
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
Engineering microbial electrocatalysis for chemical and fuel production
Rosenbaum, M. A., & Henrich, A. (2014) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2014.03.003 · Cited by 85 · 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
Redox controls metabolic robustness in the gas-fermenting acetogen Clostridium autoethanogenum
Mahamkali, V., Valgepea, K., Lemgruber, R. D. S. P., Plan, M. R., Tappel, R. C., Köpke, M., Simpson, S. D., Nielsen, L. K., & Marcellin, E. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1919531117 · Cited by 77 · see citing works
New challenges for syngas fermentation: towards production of biopolymers
Drzyzga, O., Revelles, O., Durante‐Rodríguez, G., Dı́az, E., García, J. L., & Prieto, M. A. (2015) · Journal of Chemical Technology & Biotechnology · doi:10.1002/jctb.4721 · Cited by 75 · see citing works
Metabolic strategies of marine subseafloor Chloroflexi inferred from genome reconstructions
Fincker, M., Huber, J. A., Orphan, V. J., Rappé, M. S., Teske, A., & Spormann, A. M. (2020) · Environmental Microbiology · doi:10.1111/1462-2920.15061 · Cited by 74 · see citing works
Microbial electrosynthesis with Clostridium ljungdahlii benefits from hydrogen electron mediation and permits a greater variety of products
Boto, S. T., Bardl, B., Harnisch, F., & Rosenbaum, M. A. (2023) · Green Chemistry · doi:10.1039/d3gc00471f · Cited by 73 · see citing works
A Genome-Scale Metabolic Model for Methylococcus capsulatus (Bath) Suggests Reduced Efficiency Electron Transfer to the Particulate Methane Monooxygenase
Lieven, C., Petersen, L. A. H., Jørgensen, S. B., Gernaey, K. V., Herrgård, M. J., & Sonnenschein, N. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02947 · Cited by 73 · see citing works
Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals
Jin, S., Bae, J., Song, Y., Pearcy, N., Shin, J., Kang, S., Minton, N. P., Soucaille, P., & Cho, B. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21207639 · Cited by 72 · 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
Spatiotemporal modeling of microbial metabolism
Chen, J., Gomez, J. A., Höffner, K., Phalak, P., Barton, P. I., & Henson, M. A. (2016) · BMC Systems Biology · doi:10.1186/s12918-016-0259-2 · Cited by 69 · see citing works
“The bubble column model was formulated by combining a genome-scale metabolic reconstruction of the syngas fermenting bacterium Clostridium ljungdahlii [23] with uptake kinetics for dissolved gases and reactionconvection–dispersion type equations for gaseous and dissolved substrates and synthesized metabolic byproducts.”
Method
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
Metabolic modeling of synthesis gas fermentation in bubble column reactors
Chen, J., Gomez, J. A., Höffner, K., Barton, P. I., & Henson, M. A. (2015) · Biotechnology for Biofuels · doi:10.1186/s13068-015-0272-5 · Cited by 61 · see citing works
Electron availability in CO 2 , CO and H 2 mixtures constrains flux distribution, energy management and product formation in Clostridium ljungdahlii
Hermann, M., Teleki, A., Weitz, S., Nieß, A., Freund, A., Bengelsdorf, F. R., & Takors, R. (2020) · Microbial Biotechnology · doi:10.1111/1751-7915.13625 · Cited by 61 · see citing works
Synthesis of Heterologous Mevalonic Acid Pathway Enzymes in Clostridium ljungdahlii for the Conversion of Fructose and of Syngas to Mevalonate and Isoprene
Diner, B. A., Fan, J., Scotcher, M. C., Wells, D. H., & Whited, G. M. (2017) · Applied and Environmental Microbiology · doi:10.1128/aem.01723-17 · Cited by 61 · 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
Self-citation
Gas Biological Conversions: The Potential of Syngas and Carbon Dioxide as Production Platforms
Gavala, H. N., Grimalt‐Alemany, A., Asimakopoulos, K., & Skiadas, I. V. (2021) · Waste and Biomass Valorization · doi:10.1007/s12649-020-01332-7 · Cited by 56 · see citing works
Enhancing hydrogen‐dependent growth of and carbon dioxide fixation by Clostridium ljungdahlii through nitrate supplementation
Emerson, D. F., Woolston, B. M., Liu, N., Donnelly, M., Currie, D. H., & Stephanopoulos, G. N. (2018) · Biotechnology and Bioengineering · doi:10.1002/bit.26847 · Cited by 55 · see citing works
Metabolic engineering of clostridia for the production of chemicals
Cho, C., Jang, Y., Moon, H. G., Lee, J., & Lee, S. Y. (2014) · Biofuels Bioproducts and Biorefining · doi:10.1002/bbb.1531 · Cited by 52 · see citing works
Advanced aspects of acetogens
Poehlein, A., Zeldes, B. M., Flaiz, M., Böer, T., Lüschen, A., Höfele, F., Baur, K. S., Molitor, B., Kröly, C., Wang, M., et al. (2024) · Bioresource Technology · doi:10.1016/j.biortech.2024.131913 · Cited by 51 · see citing works
Modeling ethanol production through gas fermentation: a biothermodynamics and mass transfer-based hybrid model for microbial growth in a large-scale bubble column bioreactor
Benalcázar, E. A., Noorman, H. J., Filho, R. M., & Posada, J. A. (2020) · Biotechnology for Biofuels · doi:10.1186/s13068-020-01695-y · Cited by 50 · see citing works
Nitrate Feed Improves Growth and Ethanol Production of Clostridium ljungdahlii With CO2 and H2, but Results in Stochastic Inhibition Events
Klask, C.-M., Kliem-Kuster, N., Molitor, B., & Angenent, L. T. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00724 · Cited by 49 · see citing works
Metabolic response of Clostridium ljungdahlii to oxygen exposure
Whitham, J. M., Tirado-Acevedo, O., Chinn, M. S., Pawlak, J. J., & Grunden, A. M. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.02491-15 · Cited by 47 · see citing works
Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling
Schöpping, M., Gaspar, P., Neves, A. R., Franzén, C. J., & Zeidan, A. A. (2021) · npj Systems Biology and Applications · doi:10.1038/s41540-021-00207-4 · Cited by 46 · see citing works
Metabolic modeling of clostridia: current developments and applications
Dash, S., Ng, C. Y., & Maranas, C. D. (2016) · FEMS Microbiology Letters · doi:10.1093/femsle/fnw004 · Cited by 45 · see citing works
Genome-scale analysis of syngas fermenting acetogenic bacteria reveals the translational regulation for its autotrophic growth
Song, Y., Shin, J., Jin, S., Lee, J.-K., Kim, D. R., Kim, S. C., Cho, S., & Cho, B. (2018) · BMC Genomics · doi:10.1186/s12864-018-5238-0 · Cited by 45 · see citing works
The impact of CO gradients on C. ljungdahlii in a 125 m3 bubble column: Mass transfer, circulation time and lifeline analysis
Siebler, F., Lapin, A., Hermann, M., & Takors, R. (2019) · Chemical Engineering Science · doi:10.1016/j.ces.2019.06.018 · Cited by 45 · see citing works
Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens
Feist, A. M., Nagarajan, H., Rotaru, A., Tremblay, P., Zhang, T., Nevin, K. P., Lovley, D. R., & Zengler, K. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003575 · Cited by 43 · see citing works
Self-citation
In silico metabolic engineering of Clostridium ljungdahlii for synthesis gas fermentation
Chen, J., & Henson, M. A. (2016) · Metabolic Engineering · doi:10.1016/j.ymben.2016.10.002 · Cited by 43 · see citing works
Optimization of carbon and energy utilization through differential translational efficiency
Al‐Bassam, M. M., Kim, J.-N., Zaramela, L. S., Kellman, B. P., Zúñiga, C., Wozniak, J. M., Gonzalez, D. J., & Zengler, K. (2018) · Nature Communications · doi:10.1038/s41467-018-06993-6 · Cited by 42 · see citing works
Self-citation
Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model
Islam, M. A., Zengler, K., Edwards, E. A., Mahadevan, R., & Stephanopoulos, G. (2015) · Integrative Biology · doi:10.1039/c5ib00095e · Cited by 41 · see citing works
Self-citation
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
Biological conversion of carbon monoxide and hydrogen by anaerobic culture: Prospect of anaerobic digestion and thermochemical processes combination
Andreides, D., Fliegerova, K. O., Pokorná, D., & Zábranská, J. (2021) · Biotechnology Advances · doi:10.1016/j.biotechadv.2021.107886 · Cited by 41 · see citing works
Acetyl-CoA synthesis through a bicyclic carbon-fixing pathway in gas-fermenting bacteria
Wu, C., Lo, J., Urban, C., Gao, X., Yang, B., Humphreys, J. R., Shinde, S., Wang, X., Chou, K., Maness, P., et al. (2022) · Nature Synthesis · doi:10.1038/s44160-022-00095-4 · Cited by 40 · see citing works
Physiological response of Clostridium ljungdahlii DSM 13528 of ethanol production under different fermentation conditions
Xie, B., Liu, Z., Tian, L., Li, F., & Xiaohua, C. (2014) · Bioresource Technology · doi:10.1016/j.biortech.2014.11.101 · Cited by 40 · see citing works
Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry
Zhalnina, K., Zengler, K., Newman, D. K., & Northen, T. R. (2018) · mBio · doi:10.1128/mbio.01175-18 · Cited by 40 · see citing works
Self-citation
The emerging role of aldehyde:ferredoxin oxidoreductases in microbially-catalyzed alcohol production
Nissen, L. S., & Basen, M. (2019) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2019.09.005 · Cited by 40 · see citing works
Mixotrophic co-utilization of glucose and carbon monoxide boosts ethanol and butanol productivity of continuous Clostridium carboxidivorans cultures
Vees, C. A., Herwig, C., & Pflügl, S. (2022) · Bioresource Technology · doi:10.1016/j.biortech.2022.127138 · Cited by 40 · see citing works
Production of biofuels from C 1 ‐gases with Clostridium and related bacteria—Recent advances
Fernández‐Blanco, C., Robles‐Iglesias, R., Naveira‐Pazos, C., Veiga, M. C., & Kennes, C. (2023) · Microbial Biotechnology · doi:10.1111/1751-7915.14220 · Cited by 39 · see citing works
Transcriptomic profiles of Clostridium ljungdahlii during lithotrophic growth with syngas or H2 and CO2 compared to organotrophic growth with fructose
Aklujkar, M., Leang, C., Shrestha, P. M., Shrestha, M., & Lovley, D. R. (2017) · Scientific Reports · doi:10.1038/s41598-017-12712-w · Cited by 39 · see citing works
Self-citation
Butanol production by Clostridium
Xue, C., & Cheng, C. (2019) · Advances in bioenergy · doi:10.1016/bs.aibe.2018.12.001 · Cited by 39 · see citing works
A General Model for Biofilm-Driven Microbial Electrosynthesis of Carboxylates From CO2
Cabau-Peinado, O., Straathof, A. J. J., & Jourdin, L. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.669218 · Cited by 39 · see citing works
CO2 to succinic acid – Estimating the potential of biocatalytic routes
Liebal, U. W., Blank, L. M., & Ebert, B. E. (2018) · Metabolic Engineering Communications · doi:10.1016/j.mec.2018.e00075 · Cited by 38 · see citing works
Rice straw hydrolysate to fuel and volatile fatty acid conversion by Clostridium sporogenes BE01: bio-electrochemical analysis of the electron transport mediators involved
Gottumukkala, L. D., Sukumaran, R. K., Mohan, S. V., Sajna, K. V., Sarkar, O., & Pandey, A. (2015) · Green Chemistry · doi:10.1039/c5gc00310e · Cited by 37 · 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
Engineering of vitamin prototrophy in Clostridium ljungdahlii and Clostridium autoethanogenum
Annan, F. J., Al‐Sinawi, B., Humphreys, C. M., Norman, R. O. J., Winzer, K., Köpke, M., Simpson, S. D., Minton, N. P., & Henstra, A. M. (2019) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-019-09763-6 · Cited by 37 · see citing works
Clostridium ljungdahlii as a biocatalyst in microbial electrosynthesis – Effect of culture conditions on product formation
Im, C., Valgepea, K., Modin, O., & Nygård, Y. (2022) · Bioresource Technology Reports · doi:10.1016/j.biteb.2022.101156 · Cited by 33 · see citing works
Electron carriers involved in autotrophic and heterotrophic acetogenesis in the thermophilic bacterium Thermoanaerobacter kivui
Katsyv, A., Jain, S., Basen, M., & Müller, V. (2021) · Extremophiles · doi:10.1007/s00792-021-01247-8 · Cited by 32 · see citing works
Amino acid catabolism-directed biofuel production in Clostridium sticklandii: An insight into model-driven systems engineering
Sangavai, C., & Chellapandi, P. (2017) · Biotechnology Reports · doi:10.1016/j.btre.2017.11.002 · Cited by 32 · see citing works
Genome-scale modelling of microbial metabolism with temporal and spatial resolution
Henson, M. A. (2015) · Biochemical Society Transactions · doi:10.1042/bst20150146 · Cited by 30 · 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
Genome-scale metabolic reconstruction and analysis for Clostridium kluyveri
Zou, W., Ye, G., Zhang, J., Zhao, C., Zhao, X., & Zhang, K. (2018) · Genome · doi:10.1139/gen-2017-0177 · Cited by 28 · see citing works
Incorporating hydrodynamics into spatiotemporal metabolic models of bubble column gas fermentation
Li, X., Griffin, D. W., Li, X., & Henson, M. A. (2018) · Biotechnology and Bioengineering · doi:10.1002/bit.26848 · Cited by 28 · 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
Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum
Benito-Vaquerizo, S., Olm, I. P., de Vroet, T., Schaap, P. J., Sousa, D. Z., dos Santos, V. A. P. M., & Diez, M. S. (2022) · Microbial Cell Factories · doi:10.1186/s12934-022-01841-1 · Cited by 27 · see citing works
In Silico Identification of Microbial Partners to Form Consortia with Anaerobic Fungi
Wilken, S. E., Saxena, M. C., Petzold, L. R., & O’Malley, M. (2018) · Processes · doi:10.3390/pr6010007 · Cited by 27 · see citing works
Genome‐scale model of C. autoethanogenum reveals optimal bioprocess conditions for high‐value chemical production from carbon monoxide
Norman, R. O. J., Millat, T., Schatschneider, S., Henstra, A. M., Breitkopf, R., Pander, B., Annan, F. J., Piatek, P., Hartman, H. B., Poolman, M. G., et al. (2019) · Engineering Biology · doi:10.1049/enb.2018.5003 · Cited by 27 · see citing works
Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain Design
Garcia, S., Thompson, R. A., Giannone, R. J., Dash, S., Maranas, C. D., & Trinh, C. T. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.00772 · Cited by 27 · see citing works
Model-based driving mechanism analysis for butyric acid production in Clostridium tyrobutyricum
Feng, J., Guo, X., Cai, F., Fu, H., & Wang, J. (2022) · Biotechnology for Biofuels and Bioproducts · doi:10.1186/s13068-022-02169-z · Cited by 26 · see citing works
Flux balance analysis of metabolic networks for efficient engineering of microbial cell factories
Sen, P. (2022) · Biotechnology and Genetic Engineering Reviews · doi:10.1080/02648725.2022.2152631 · Cited by 26 · see citing works
13C-metabolic flux analysis of Clostridium ljungdahlii illuminates its core metabolism under mixotrophic culture conditions
Dahle, M. L., Papoutsakis, E. T., & Antoniewicz, M. R. (2022) · Metabolic Engineering · doi:10.1016/j.ymben.2022.03.011 · Cited by 25 · see citing works
Biological acetate production from carbon dioxide by Acetobacterium woodii and Clostridium ljungdahlii: The effect of cell immobilization
Cheng, H., Syu, J.-C., Tien, S.-Y., & Whang, L. (2018) · Bioresource Technology · doi:10.1016/j.biortech.2018.04.069 · Cited by 25 · see citing works
Modeling of nitrogen fixation and polymer production in the heterotrophic diazotroph Azotobacter vinelandii DJ
Tec-Campos, D., Zúñiga, C., Passi, A., Toro, J. D., Tibocha‐Bonilla, J. D., Zepeda, A., Betenbaugh, M. J., & Zengler, K. (2020) · Metabolic Engineering Communications · doi:10.1016/j.mec.2020.e00132 · Cited by 25 · see citing works
Self-citation
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
Dos and don’ts for scaling up gas fermentations
Puiman, L., Bokelmann, C., Simpson, S. D., Spormann, A. M., & Takors, R. (2025) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2025.103294 · Cited by 23 · see citing works
The Metabolism of Clostridium ljungdahlii in Phosphotransacetylase Negative Strains and Development of an Ethanologenic Strain
Lo, J., Humphreys, J. R., Jack, J., Urban, C., Magnusson, L. R., Xiong, W., Gu, Y., Ren, Z. J., & Maness, P. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.560726 · Cited by 23 · see citing works
Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds
Canto-Encalada, G., Tec-Campos, D., Tibocha‐Bonilla, J. D., Zengler, K., Zepeda, A., & Zúñiga, C. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1009828 · Cited by 23 · see citing works
Self-citation
Cancer Cell Metabolism as New Targets for Novel Designed Therapies
de Mas, I. M., Aguilar, E., Jayaraman, A., Polat, I. H., Martín-Bernabé, A., Bharat, R., Foguet, C., Milà, E., Papp, B., Centelles, J. J., et al. (2014) · Future Medicinal Chemistry · doi:10.4155/fmc.14.119 · Cited by 23 · see citing works
Metabolic modeling of bacterial co-culture systems predicts enhanced carbon monoxide-to-butyrate conversion compared to monoculture systems
Li, X., & Henson, M. A. (2019) · Biochemical Engineering Journal · doi:10.1016/j.bej.2019.107338 · Cited by 22 · see citing works
Systems-Level Modeling for CRISPR-Based Metabolic Engineering
Cardiff, R. A. L., Carothers, J. M., Zalatan, J. G., & Sauro, H. M. (2024) · ACS Synthetic Biology · doi:10.1021/acssynbio.4c00053 · Cited by 21 · see citing works
Deep Crustal Communities of the Juan de Fuca Ridge Are Governed by Mineralogy
Smith, A. R., Fisk, M. R., Thurber, A. R., Flores, G. E., Mason, O. U., Popa, R., & Colwell, F. S. (2016) · Geomicrobiology Journal · doi:10.1080/01490451.2016.1155001 · Cited by 21 · see citing works
Clostridium butyricum maximizes growth while minimizing enzyme usage and ATP production: metabolic flux distribution of a strain cultured in glycerol
Serrano‐Bermúdez, L. M., Barrios, A. F. G., Maranas, C. D., & Castaño, D. M. (2017) · BMC Systems Biology · doi:10.1186/s12918-017-0434-0 · Cited by 20 · 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
Self-citation
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
Insight into acetogens metabolism through the use of thermodynamic metabolic flux analysis
Mahamkali, V. (2021) · The University of Queensland · doi:10.14264/4dae3e1
Using a metabolic model of Acetobacterium woodii for insights into its utility for biotechnological purposes
Mesfin, N., Fell, D. A., & Mesfin, N. (2019) · Access Microbiology · doi:10.1099/acmi.ac2019.po0361 · Cited by 1 · see citing works
Structural Metabolic Modelling of the Acetogen Acetobacterium woodii
Mesfin, N. (2020) · Radar (Oxford Brookes University) · doi:10.24384/m6b1-3933 · Cited by 1 · see citing works

Authors: Nagarajan, H., Sahin, M., Nogales, J., Latif, H., Lovley, D. R., Ebrahim, A., & Zengler, K.
Affiliations: University of California San Diego (US)
University of Massachusetts Amherst (US)
Corresponding author: Zengler, Karsten
ORCID: Nogales, Juan
Latif, Haythem
Lovley, Derek R
Ebrahim, Ali
Zengler, Karsten
Venue: Microbial Cell Factories
Publisher: Springer Science and Business Media LLC
Published: 2013-11-25
Volume: 12
Issue: 1
Pages: 118-118
ISSN: 1475-2859 (ISSN-L)
DOI: 10.1186/1475-2859-12-118
PMC: PMC4222884
OpenAlex: W2038304602
Cited by: 170
References: 52
Citations by year: 2026: 8 · 2025: 8 · 2024: 10 · 2023: 9 · 2022: 23 · 2021: 11 · 2020: 13 · 2019: 13 · 2018: 19 · 2017: 19 · 2016: 11 · 2015: 13 · 2014: 13
FWCI: 5.52
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
Locations: Microbial Cell Factories (publishedVersion, cc-by)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
eScholarship (California Digital Library) (submittedVersion)
Funders: National Science Foundation (1144086)
U.S. Department of Energy (DEAR0000159, DEAR0000087, DESC0004917)
Advanced Research Projects Agency - Energy (DE-AR0000159)
Office of Science
University of California, San Diego
Advanced Research Projects Agency
National Institute of General Medical Sciences (U01GM102098)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
Physical Sciences › Engineering › Biomedical Engineering › Biofuel production and bioconversion
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Keywords: Clostridium ljungdahlii, genome-scale metabolic models, autotrophic growth, energy conservation, CO2 fixation, metabolic engineering, biofuels
MeSH terms: Acetates, Clostridium, Genome, Metabolic Networks and Pathways, Biofuels, Metabolic Engineering

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

Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii

Abstract

Integrity signals

Claims the paper makes

Claims other papers make about this one

Self-check

Cites

Cited by

Related

Record

About these checks