Your browser does not support JavaScript!
http://iet.metastore.ingenta.com
1887

access icon openaccess Genome-scale model of C. autoethanogenum reveals optimal bioprocess conditions for high-value chemical production from carbon monoxide

Loading full text...

Full text loading...

/deliver/fulltext/enb/3/2/ENB.2018.5003.html;jsessionid=2mn2jba96ldbt.x-iet-live-01?itemId=%2fcontent%2fjournals%2f10.1049%2fenb.2018.5003&mimeType=html&fmt=ahah

References

    1. 1)
      • 54. Hempfling, W.P., Mainzer, S.E.: ‘Effects of varying the carbon source limiting growth on yield and maintenance characteristics of Escherichia coli in continuous culture’, J. Bacteriol., 1975, 123, (3), pp. 10761087.
    2. 2)
      • 10. Schiel-Bengelsdorf, B., Dürre, P.: ‘Pathway engineering and synthetic biology using acetogens’, FEBS Lett., 2012, 586, (15), pp. 21912198.
    3. 3)
      • 67. Holzhütter, H.G.: ‘The generalized flux-minimization method and its application to metabolic networks affected by enzyme deficiencies’, Biosystems, 2006, 83, (2–3), pp. 98107.
    4. 4)
      • 41. Kracke, F., Virdis, B., Bernhardt, P.V., et al: ‘Redox dependent metabolic shift in Clostridium autoethanogenum by extracellular electron supply’, Biotechnol. Biofuels, 2016, 9, (1), p. 249.
    5. 5)
      • 15. Abrini, J., Naveau, H., Nyns, E.J.: ‘Clostridium autoethanogenum, sp. nov., an anaerobic bacterium that produces ethanol from carbon monoxide’, Arch. Microbiol., 1994, 161, (4), pp. 345351.
    6. 6)
      • 58. Cuevas, D.A., Edirisinghe, J., Henry, C.S., et al: ‘From DNA to FBA: how to build your own genome-scale metabolic model’, Front. Microbiol., 2016, 7, p. 907.
    7. 7)
      • 28. Köpke, M., Held, C., Hujer, S., et al: ‘Clostridium ljungdahlii represents a microbial production platform based on syngas’, Proc. Natl. Acad. Sci., 2010, 107, (29), pp. 1308713092.
    8. 8)
      • 29. Schatschneider, S., Abdelrazig, S., Safo, L., et al: ‘Quantitative isotope-dilution high-resolution-mass-spectrometry analysis of multiple intracellular metabolites in Clostridium autoethanogenum with uniformly 13C-labeled standards derived from Spirulina’, Anal. Chem., 2018, 90, (7), pp. 44704477.
    9. 9)
      • 57. Fell, D., Cornish-Bowden, A.: ‘Understanding the control of metabolism’, vol. 2, (Portland Press London, England, 1997).
    10. 10)
      • 27. Bruno-Barcena, J.M., Chinn, M.S., Grunden, A.M.: ‘Genome sequence of the autotrophic acetogen Clostridium autoethanogenum JA1-1 strain DSM 10061, a producer of ethanol from carbon monoxide’, Genome Announcements, 2013, 1, (4), pp. e0062813.
    11. 11)
      • 51. Milne, C.B., Eddy, J.A., Raju, R., et al: ‘Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052’, BMC Syst. Biol., 2011, 5, (1), p. 130.
    12. 12)
      • 62. Strang, G.: ‘Linear algebra and its applications’ (Thomson Learning, Boston, MA, 1988).
    13. 13)
      • 34. Poolman, M.G.: ‘Scrumpy: metabolic modelling with Python’, IEE Proc. Syst. Biol., 2006, 153, (5), pp. 375378.
    14. 14)
      • 61. Palsson, B.Ø.: ‘Systems biology: properties of reconstructed networks’ (Cambridge University Press, New York, NY, 2006).
    15. 15)
      • 11. Biegel, E., Schmidt, S., González, J.M., et al: ‘Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes’, Cell. Mol. Life Sci., 2011, 68, (4), pp. 613634.
    16. 16)
      • 43. Brown, S., Santa Maria, J.P.Jr., Walker, S.: ‘Wall teichoic acids of Gram-positive bacteria’, Annu. Rev. Microbiol., 2013, 67, pp. 313336.
    17. 17)
      • 46. Lee, J., Yun, H., Feist, A.M., et al: ‘Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network’, Appl. Microbiol. Biotechnol., 2008, 80, (5), pp. 849862.
    18. 18)
      • 40. Schuchmann, K., Müller, V.: ‘Autotrophy at the thermo dynamic limit of life: a model for energy conservation in acetogenic bacteria’, Nat. Rev. Microbiol., 2014, 12, (12), pp. 809821.
    19. 19)
      • 31. Fell, D.A., Poolman, M.G., Gevorgyan, A.: ‘Building and analysing genome-scale metabolic models’, Biochem. Soc. Trans., 2010, 38, (5), pp. 11971201.
    20. 20)
      • 74. Claassen, P., Van Lier, J., Contreras, A.L., et al: ‘Utilisation of biomass for the supply of energy carriers’, Appl. Microbiol. Biotechnol., 1999, 52, (6), pp. 741755.
    21. 21)
      • 2. Pachauri, R.K., Allen, M.R., Barros, V.R., et al: ‘Climate change 2014: synthesis report. Contribution of working groups I, II and III to the fifth assessment report of the intergovernmental panel on climate change’ (IPCC, Switzerland, 2014).
    22. 22)
      • 44. Feist, A.M., Palsson, B.Ø.: ‘The biomass objective function’, Curr. Opin. Microbiol., 2010, 13, (3), pp. 344349.
    23. 23)
      • 21. Dash, S., Ng, C.Y., Maranas, C.D.: ‘Metabolic modeling of Clostridia: current developments and applications’, FEMS Microbiol. Lett., 2016, 363, (4), p. fnw004.
    24. 24)
      • 14. Köpke, M., Mihalcea, C., Liew, F., et al: ‘2, 3-Butanediol production by acetogenic bacteria, an alternative route to chemical synthesis, using industrial waste gas’, Appl. Environ. Microbiol., 2011, 77, (15), pp. 54675475.
    25. 25)
      • 7. Ljungdahl, L.G., Wood, H.G.: ‘Incorporation of c14 from carbon dioxide into sugar phosphates, carboxylic acids, and amino acids by Clostridium thermoaceticum’, J. Bacteriol., 1965, 89, (4), pp. 10551064.
    26. 26)
      • 26. http://sbrc-seek.nottingham.ac.uk/data_files/1?version=1.
    27. 27)
      • 24. Brown, S.D., Nagaraju, S., Utturkar, S., et al: ‘Comparison of single molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia’, Biotechnol. Biofuels, 2014, 7, (1), p. 40.
    28. 28)
      • 71. Breitkopf, R.: ‘Understanding the C4 dicarboxylic acid metabolism in Clostridium autoethanogenum’. PhD thesis, University of Nottingham, 2018.
    29. 29)
      • 1. Armaroli, N., Balzani, V.: ‘The legacy of fossil fuels’, Chem. Asian J., 2011, 6, (3), pp. 768784.
    30. 30)
      • 56. Schuster, S., Fell, D.A., Dandekar, T.: ‘A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks’, Nat. Biotechnol., 2000, 18, (3), p. 326.
    31. 31)
      • 68. Ebrahim, A., Lerman, J., Palsson, B., et al: ‘COBRApy: constraints-based reconstruction and analysis for Python’, BMC Syst. Biol., 2013, 7, (1), p. 74.
    32. 32)
      • 42. Blom, J., Albaum, S.P., Doppmeier, D., et al: ‘EDGAR: a software framework for the comparative analysis of prokaryotic genomes’, BMC Bioinformatics, 2009, 10, (1), p. 154.
    33. 33)
      • 36. Wang, S., Huang, H., Kahnt, J., et al: ‘NADP-specific electron-bifurcating [FeFe]-hydrogenase in a functional complex with for mate dehydrogenase in Clostridium autoethanogenum grown on CO’, J. Bacteriol., 2013, 195, (19), pp. 43734386.
    34. 34)
      • 12. Yoshida, M., Muneyuki, E., Hisabori, T.: ‘ATP synthase – a marvellous rotary engine of the cell’, Nat. Rev. Mol. Cell Biol., 2001, 2, (9), p. 669.
    35. 35)
      • 8. Ljungdahl, L.G., Wood, H.G.: ‘Total synthesis of acetate from CO2 by heterotrophic bacteria’, Annu. Rev. Microbiol., 1969, 23, (1), pp. 515538.
    36. 36)
      • 19. Valgepea, K., de Souza Pinto Lemgruber, R., Meaghan, K., et al: ‘Maintenance of ATP homeostasis triggers metabolic shifts in gas-fermenting acetogens’, Cell Syst., 2017, 4, (5), pp. 505515.e5.
    37. 37)
      • 70. Cotter, J.L., Chinn, M.S., Grunden, A.M.: ‘Ethanol and acetate production by Clostridium ljungdahlii and Clostridium autoethanogenum using resting cells’, Bioprocess. Biosyst. Eng., 2009, 32, (3), pp. 369380.
    38. 38)
      • 75. Levin, D.B., Pitt, L., Love, M.: ‘Biohydrogen production: prospects and limitations to practical application’, Int. J. Hydrog. Energy, 2004, 29, (2), pp. 173185.
    39. 39)
      • 38. Schuster, S., Hilgetag, C.: ‘On elementary flux modes in biochemical reaction systems at steady state’, J. Biol. Syst., 1994, 2, (2), pp. 165182.
    40. 40)
      • 16. Henstra, A.M., Sipma, J., Rinzema, A., et al: ‘Microbiology of synthesis gas fermentation for biofuel production’, Curr. Opin. Biotechnol., 2007, 18, (3), pp. 200206.
    41. 41)
      • 72. Valgepea, K., Lemgruber, R.S.P., Abdalla, T., et al: ‘H2 drives metabolic rearrangements in gas-fermenting Clostridium autoethanogenum’, Biotechnol. Biofuels, 2018, 11, (1), p. 55.
    42. 42)
      • 39. Meier, T., Ferguson, S.A., Cook, G.M., et al: ‘Structural investigations of the membrane-embedded rotor ring of the F1Fo-ATPase from Clostridium paradoxum’, J. Bacteriol., 2006, 188, (22), pp. 77597764.
    43. 43)
      • 17. Marcellin, E., Behrendorff, J.B., Nagaraju, S., et al: ‘Low carbon fuels and commodity chemicals from waste gases – systematic approach to understand energy metabolism in a model acetogen’, Green Chem., 2016, 18, pp. 30203028.
    44. 44)
      • 20. Valgepea, K., Loi, K.Q., Behrendorff, J.B., et al: ‘Arginine deiminase pathway provides ATP and boosts growth of the gas-fermenting acetogen Clostridium autoethanogenum’, Metab. Eng., 2017, 41, pp. 202211.
    45. 45)
      • 49. Li, G.W., Burkhardt, D., Gross, C., et al: ‘Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources’, Cell, 2014, 157, (3), pp. 624635.
    46. 46)
      • 23. Johnson, M.J., Peterson, W.H., Fred, E.B.: ‘Oxidation and reduction relations between substrate and products in the acetone-butyl alcohol fermentation’, J. Biol. Chem., 1931, 91, (2), pp. 569591.
    47. 47)
      • 22. Humphreys, C.M., McLean, S., Schatschneider, S., et al: ‘Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium’, BMC Genomics, 2015, 16, (1), p. 1.
    48. 48)
      • 45. Pramanik, J., Keasling, J.: ‘Stoichiometric model of Escherichia coli metabolism: incorporation of growth rate dependent biomass composition and mechanistic energy requirements’, Biotechnol. Bioeng., 1997, 56, (4), pp. 398421.
    49. 49)
      • 5. Norman, R.O., Millat, T., Winzer, K., et al: ‘Progress towards platform chemical production using Clostridium autoethanogenum’, Biochem. Soc. Trans., 2018, 46, (3), pp. 523535.
    50. 50)
      • 50. Nagarajan, H., Sahin, M., Nogales, J., et al: ‘Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii’, Microbial Cell Factories, 2013, 12, (1), p. 1.
    51. 51)
      • 63. Schellenberger, J., Que, R., Fleming, R.M., et al: ‘Quantitative prediction of cellular metabolism with constraint-based models: the COBRA toolbox v2. 0’, Nat. Protoc., 2011, 6, (9), pp. 12901307.
    52. 52)
      • 47. Senger, R.S., Papoutsakis, E.T.: ‘Genome-scale model for Clostridium acetobutylicum: part I. Metabolic network resolution and analysis’, Biotechnol. Bioeng., 2008, 101, (5), pp. 10531071.
    53. 53)
      • 32. Hartman, H.B., Fell, D.A., Rossell, S., et al: ‘Identification of potential drug targets in Salmonella enterica sv. typhimurium using metabolic modelling and experimental validation’, Microbiology, 2014, 160, (6), pp. 12521266.
    54. 54)
      • 59. Hartman, H.B.: ‘Genome-scale metabolic modelling of Salmonella and Lactococcus species’. PhD thesis, Oxford Brookes University, 2013.
    55. 55)
      • 48. Senger, R.S., Papoutsakis, E.T.: ‘Genome-scale model for Clostridium acetobutylicum: part II. Development of specific proton flux states and numerically determined sub-systems’, Biotechnol. Bioeng., 2008, 101, (5), pp. 10531071.
    56. 56)
      • 25. Karp, P.D., Paley, S., Romero, P.: ‘The pathway tools software’, Bioinformatics, 2002, 18, (suppl 1), pp. S225S232.
    57. 57)
      • 37. Schuster, S., Dandekar, T., Fell, D.A.: ‘Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering’, Trends Biotechnol., 1999, 17, (2), pp. 5360.
    58. 58)
      • 64. Varma, A., Palsson, B.Ø.: ‘Metabolic flux balancing: basic concepts, scientific and practical use’, Nat. Biotechnol., 1994, 12, (10), p. 994.
    59. 59)
      • 65. Schuetz, R., Kuepfer, L., Sauer, U.: ‘Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli’, Mol. Syst. Biol., 2007, 3, (1), p. 119.
    60. 60)
      • 52. Bainotti, A., Nishio, N.: ‘Growth kinetics of Acetobacterium sp. on methanol-formate in continuous culture’, J. Appl. Microbiol., 2000, 88, (2), pp. 191201.
    61. 61)
      • 69. Machado, D., Andrejev, S., Tramontano, M., et al: ‘Fast automated reconstruction of genome-scale metabolic models for microbial species and communities’, Nucleic Acids Res., 2018, 46, (15), pp. 75427553.
    62. 62)
      • 73. Angenent, L.T., Karim, K., Al-Dahhan, M.H., et al: ‘Production of bioenergy and biochemicals from industrial and agricultural wastewater’, Trends Biotechnol., 2004, 22, (9), pp. 477485.
    63. 63)
      • 3. Doran, P.M.: ‘Bioprocess engineering principles’ (Academic Press, Waltham, MA, 1995).
    64. 64)
      • 76. Le Novère, N., Bornstein, B., Broicher, A., et al: ‘Biomodels database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems’, Nucleic Acids Res., 2006, 34, (suppl_1), pp. D689D691.
    65. 65)
      • 4. Heijstra, B.D., Leang, C., Juminaga, A.: ‘Gas fermentation: cellular engineering possibilities and scale up’, Microb. Cell Fact., 2017, 16, (1), p. 60.
    66. 66)
      • 35. Mock, J., Zheng, Y., Mueller, A.P., et al: ‘Energy conservation associated with ethanol formation from H2 and CO2 in Clostridium autoethanogenum involving electron bifurcation’, J. Bacteriol., 2015, 197, (18), pp. 29652980.
    67. 67)
      • 60. Pfeiffer, T., Sánchez-Valdenebro, I., Nuño, J., et al: ‘METATOOL: for studying metabolic networks’, Bioinformatics, 1999, 15, (3), pp. 251257.
    68. 68)
      • 18. Oberhardt, M.A., Palsson, B.Ø., Papin, J.A.: ‘Applications of genome-scale metabolic reconstructions’, Mol. Syst. Biol., 2009, 5, (1), p. 320.
    69. 69)
      • 6. Liew, F., Martin, M.E., Tappel, R.C., et al: ‘Gas fermentation – a flexible platform for commercial scale production of low carbon-fuels and chemicals from waste and renewable feedstocks’, Front. Microbiol., 2016, 7, p. 694.
    70. 70)
      • 55. Verduyn, C., Postma, E., Scheffers, W.A., et al: ‘Energetics of Saccharomyces cerevisiae in anaerobic glucose-limited chemostat cultures’, Microbiology, 1990, 136, (3), pp. 405412.
    71. 71)
      • 66. Holzhütter, H.G.: ‘The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks’, Eur. J. Biochem., 2004, 271, (14), pp. 29052922.
    72. 72)
      • 9. Ragsdale, S.W., Pierce, E.: ‘Acetogenesis and the Wood–Ljungdahl pathway of CO2 fixation’, Biochim. Biophys. Acta Proteins Proteomics, 2008, 1784, (12), pp. 18731898.
    73. 73)
      • 13. Reidlinger, J., Müller, V.: ‘Purification of ATP synthase from Acetobacterium woodii and identification as a na+-translocating f1fo-type enzyme’, Eur. J. Biochem., 1994, 223, (1), pp. 275283.
    74. 74)
      • 53. Oh, Y.K., Palsson, B.Ø., Park, S.M., et al: ‘Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high throughput phenotyping and gene essentiality data’, J. Biol. Chem., 2007, 282, (39), pp. 2879128799.
    75. 75)
      • 30. Caspi, R., Foerster, H., Fulcher, C.A., et al: ‘The Meta-Cyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases’, Nucleic Acids Res., 2008, 36, (suppl 1), pp. D623D631.
    76. 76)
      • 33. Gevorgyan, A., Poolman, M.G., Fell, D.A.: ‘Detection of stoichiometric inconsistencies in biomolecular models’, Bioinformatics, 2008, 24, (19), pp. 22452251.
http://iet.metastore.ingenta.com/content/journals/10.1049/enb.2018.5003
Loading

Supplementary material

Related content

content/journals/10.1049/enb.2018.5003
pub_keyword,iet_inspecKeyword,pub_concept
6
6
Loading
This is a required field
Please enter a valid email address