Improving fermentative biomass-derived H2-production by engineering microbial metabolism

International Journal of Hydrogen Energy

Volumn 33, Issue 19, 2008, Pages 5122-5130

  Jones, Patrik R ^a  

^a FUJIREBIO INC   (Japan)

Author keywords

Biomass; Engineering of microbial metabolism; Fermentation; Hydrogen production; Review

Indexed keywords

BIOCHEMICAL ENGINEERING; BIOCHEMISTRY; BIOLOGICAL MATERIALS; BIOMASS; GAS FUEL MANUFACTURE; GENETIC ENGINEERING; HYDROGEN; METABOLISM; NONMETALS; RENEWABLE ENERGY RESOURCES; SUGAR (SUCROSE); SUGARS; TECHNOLOGY;

COMMERCIAL VIABILITY; END PRODUCTS; ENGINEERING OF MICROBIAL METABOLISM; FEEDBACK INHIBITION; FERMENTATION; FERMENTATIVE HYDROGEN PRODUCTION; MAJOR FACTOR; MICROBIAL FERMENTATION; MICROBIAL METABOLISM; PRODUCTION OF HYDROGEN; REVIEW;

HYDROGEN PRODUCTION;

EID: 52049098684     PISSN: 03603199     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijhydene.2008.05.004     Document Type: Article

References (81)

1. Melis A., Zhang L., Forestier M., Ghirardi M.L., and Seibert M. Sustained photobiological hydrogen gas production upon reversible inactivation of oxygen evolution in the green alga Chlamydomonas reinhardtii. Plant Physiol 122 (2000) 127-136
2. 2 production in microorganisms. Appl Microbiol Biotechnol 72 (2006) 442-449
3. Hallenbeck P.C. Fundamentals of the fermentative production of hydrogen. Water Sci Technol 52 (2005) 21-29
4. Logan B.E. Extracting hydrogen and electricity from renewable resources. Environ Sci Technol 38 (2004) 160A-167A
5. Service RF. The hydrogen backlash. Science 305 (2004) 958-961
6. Hill J., Nelson E., Tilman D., Polasky S., and Tiffany D. Environmental, economic, and energetic costs and benefits of biodiesel and ethanol biofuels. Proc Natl Acad Sci U S A 103 (2006) 11206-11210
7. Pimentel D., Patzek T., and Cecil G. Ethanol production: energy, economic, and environmental losses. Rev Environ Contam Toxicol 189 (2007) 25-41
8. Service R.F. Cellulosic ethanol. Biofuel researchers prepare to reap a new harvest. Science 315 (2007) 1488-1491
9. Benemann J. Hydrogen biotechnology: progress and prospects. Nat Biotechnol 14 (1996) 1101-1103
10. Angenent L.T., Karim K., Al-Dahhan M.H., Wrenn B.A., and Domiguez-Espinosa R. Production of bioenergy and biochemicals from industrial and agricultural wastewater. Trends Biotechnol 22 (2004) 477-485
11. de Vrije T., Mars A.E., Budde M.A., Lai M.H., Dijkema C., de Waard P., and Claassen P.A. Glycolytic pathway and hydrogen yield studies of the extreme thermophile Caldicellulosiruptor saccharolyticus. Appl Microbiol Biotechnol 74 (2007) 1358-1367
12. van Groenestijn J.W., Hazewinkel J.H.O., Nienoord M., and Bussmann P.J.T. Energy aspects of biological hydrogen production in high rate bioreactors operated in the thermophilic temperature range. Int J Hydrogen Energy 27 (2002) 1141-1147
13. Underwood S.A., Buszko M.L., Shanmugam K.T., and Ingram L.O. Lack of protective osmolytes limits final cell density and volumetric productivity of ethanologenic Escherichia coli KO11 during xylose fermentation. Appl Environ Microbiol 70 (2004) 2734-2740
14. Chen F., and Dixon R.A. Lignin modification improves fermentable sugar yields for biofuel production. Nat Biotechnol 25 (2007) 759-761
15. van Niel E.W., Claassen P.A., and Stams A.J. Substrate and product inhibition of hydrogen production by the extreme thermophile, Caldicellulosiruptor saccharolyticus. Biotechnol Bioeng 81 (2003) 255-262
16. Yoshida A., Nishimura T., Kawaguchi H., Inui M., and Yukawa H. Enhanced hydrogen production from glucose using ldh- and frd-inactivated Escherichia coli strains. Appl Microbiol Biotechnol 73 (2006) 67-72
17. Nealson K.H., and Conrad P.G. Life: past, present and future. Philos Trans R Soc Lond B Biol Sci 354 (1999) 1923-1939
18. Valentine D.L. Adaptations to energy stress dictate the ecology and evolution of the Archaea. Nat Rev Microbiol 5 (2007) 316-323
19. Unden G., and Bongaerts J. Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors. Biochim Biophys Acta 1320 (1997) 217-234
20. Garcia J.L., Patel B.K., and Ollivier B. Taxonomic, phylogenetic, and ecological diversity of methanogenic Archaea. Anaerobe 6 (2000) 205-226
21. Canfield D.E., Rosing M.T., and Bjerrum C. Early anaerobic metabolisms. Philos Trans R Soc Lond B Biol Sci 361 (2006) 1819-1834
22. Alberty R.A. Standard apparent reduction potentials for biochemical half reactions as function of pH and ionic strength. Arch Biochem Biophys 389 (2001) 94-109
23. Odom J.M., and Peck H.D. Hydrogen cycling as a general mechanism for energy coupling in the sulfate reducing bacteria, Desulfovibrio sp. FEMS Microbiol Lett 12 (1981) 47-50
24. King P.W., and Przybyla A.E. Response of hya expression to external pH in Escherichia coli. J Bacteriol 181 (1999) 5250-5256
25. Maeda T., Sanchez-Torres V., and Wood T.K. Escherichia coli hydrogenase 3 is a reversible enzyme possessing hydrogen uptake and synthesis activities. Appl Microbiol Biotechnol 76 (2007) 1035-1042
26. Vignais P.M., Billoud B., and Meyer J. Classification and phylogeny of hydrogenases. FEMS Microbiol Rev 25 (2001) 455-501
27. Blaut M. Metabolism of methanogens. Antonie Van Leeuwenhoek 66 (1994) 187-208
28. 2-pathways. Microbial Biotechnology, in press doi:10.1111/j.1751-7915.2008.00033.x.
29. Eriksen NT, Nielsen TM, Iversen N. Hydrogen production in anaerobic and microaerobic Thermotoga neapolitana. Biotechnol Lett in press. doi:10.1007/s10529-007-9520-5.
30. van Niel E.W.J., Budde M.A.W., de Haas G.G., van der Wal F.J., Claassen P.A.M., and Stams A.J.M. Distinctive properties of high hydrogen producing extreme thermophiles, Caldicellulosiruptor saccharolyticus and Thermotoga elfii. Int J Hydrogen Energy 27 (2002) 1391-1398
31. Soboh B., Linder D., and Hedderich R. A multisubunit membrane-bound [NiFe] hydrogenase and an NADH-dependent Fe-only hydrogenase in the fermenting bacterium Thermoanaerobacter tengcongensis. Microbiology 150 (2004) 2451-2463
32. Verhagen M.F., O'Rourke T., and Adams M.W. The hyperthermophilic bacterium, Thermotoga maritima, contains an unusually complex iron-hydrogenase: amino acid sequence analyses versus biochemical characterization. Biochim Biophys Acta 1412 (1999) 212-229
33. Verhees C.H., Kengen S.W., Tuininga J.E., Schut G.J., Adams M.W., De Vos W.M., and Van Der Oost J. The unique features of glycolytic pathways in Archaea. Biochem J 375 (2003) 231-246
34. Available form:. http://cmr.tigr.org/tigr-scripts/CMR/GenomePage.cgi?database=btm
35. Wilson D.F. Evaluation of enzyme systems and their regulation: the inapplicability of irreversible thermodynamics. Biochim Biophys Acta 616 (1980) 371-380
36. Sapra R., Bagramyan K., and Adams M.W. A simple energy-conserving system: proton reduction coupled to proton translocation. Proc Natl Acad Sci U S A 100 (2003) 7545-7550
37. Calteau A., Gouy M., and Perriere G. Horizontal transfer of two operons coding for hydrogenases between bacteria and Archaea. J Mol Evol 60 (2005) 557-565
38. Nakashimada Y., Rachman M.A., Kakizono T., and Nishio N. Hydrogen production of Enterobacter aerogenes altered by extracellular and intracellular redox states. Int J Hydrogen Energy 27 (2002) 1399-1405
39. 2 consumption by Escherichia coli coupled via hydrogenase 1 or hydrogenase 2 to different terminal electron acceptors. FEMS Microbiol Lett 202 (2001) 121-124
40. Laurinavichene T.V., Zorin N.A., and Tsygankov A.A. Effect of redox potential on activity of hydrogenase 1 and hydrogenase 2 in Escherichia coli. Arch Microbiol 178 (2002) 437-442
41. Ito T., Nakashimada Y., Kakizono T., and Nishio N. High-yield production of hydrogen by Enterobacter aerogenes mutants with decreased alpha-acetolactate synthase activity. J Biosci Bioeng 97 (2004) 227-232
42. Rachman M.A., Furutani Y., Nakashimada Y., Kakizono T., and Nishio N. Enhanced hydrogen production in altered mixed acid fermentation of glucose by Enterobacter aerogenes. J Ferment Bioeng 83 (1997) 358-363
43. 2 production by Enterobacter cloacae. Biotechnol Lett 23 (2001) 537-541
44. Morimoto K., Kimura T., Sakka K., and Ohmiya K. Overexpression of a hydrogenase gene in Clostridium paraputrificum to enhance hydrogen gas production. FEMS Microbiol Lett 246 (2005) 229-234
45. Yoshida A., Nishimura T., Kawaguchi H., Inui M., and Yukawa H. Enhanced hydrogen production from formic acid by formate hydrogen lyase-overexpressing Escherichia coli strains. Appl Environ Microbiol 71 (2005) 6762-6768
46. Akhtar M.K., and Jones P.R. Engineering of a synthetic hydF-hydE-hydG-hydA operon for biohydrogen production. Anal Biochem 373 (2008) 170-172
47. Thauer R.K. Citric-acid cycle, 50 years on. Modifications and an alternative pathway in anaerobic bacteria. Eur J Biochem 176 (1988) 497-508
48. Alberty R.A. Thermodynamics of biochemical reactions (2003), John Wiley & Sons, Inc., Hoboken, NJ
49. Woodward J., Orr M., Cordray K., and Greenbaum E. Enzymatic production of biohydrogen. Nature 405 (2000) 1014-1015
50. Koku H., Eroglu I., Gunduz U., Yucel M., and Turker L. Aspects of the metabolism of hydrogen production by Rhodobacter sphaeroides. Int J Hydrogen Energy 27 (2002) 1315-1329
51. Oh Y.-K., Seol E.-H., Kim M.S.M.-S., and Park S. Photoproduction of hydrogen from acetate by a chemoheterotrophic bacterium Rhodopseudomonas palustris P4. Int J Hydrogen Energy 29 (2004) 1115-1121
52. Kim M.-S., Baek J.-S., Yun Y.-S., Jun Sim S., Park S., and Kim S.-C. Hydrogen production from Chlamydomonas reinhardtii biomass using a two-step conversion process: anaerobic conversion and photosynthetic fermentation. Int J Hydrogen Energy 31 (2006) 812-816
53. Liu H., Grot S., and Logan B.E. Electrochemically assisted microbial production of hydrogen from acetate. Environ Sci Technol 39 (2005) 4317-4320
54. Rozendal R.A., Hamelers H.V.M., Euverink G.J.W., Metz S.J., and Buisman C.J.N. Principle and perspectives of hydrogen production through biocatalyzed electrolysis. Int J Hydrogen Energy 31 (2006) 1632-1640
55. Cheng S., and Logan B.E. Sustainable and efficient biohydrogen production via electrohydrogenesis. Proc Natl Acad Sci U S A 104 (2007) 18871-18873
56. Ragauskas A.J., Williams C.K., Davison B.H., Britovsek G., Cairney J., Eckert C.A., Frederick Jr. W.J., Hallett J.P., Leak D.J., Liotta C.L., Mielenz J.R., Murphy R., Templer R., and Tschaplinski T. The path forward for biofuels and biomaterials. Science 311 (2006) 484-489
57. Boddiger D. Boosting biofuel crops could threaten food security. Lancet 370 (2007) 923-924
58. Lynd L.R., van Zyl W.H., McBride J.E., and Laser M. Consolidated bioprocessing of cellulosic biomass: an update. Curr Opin Biotechnol 16 (2005) 577-583
59. Otero J.M., Panagiotou G., and Olsson L. Fueling industrial biotechnology growth with bioethanol. Adv Biochem Eng Biotechnol 108 (2007) 1-40
60. van der Rest B., Danoun S., Boudet A.M., and Rochange S.F. Down-regulation of cinnamoyl-CoA reductase in tomato (Solanum lycopersicum L.) induces dramatic changes in soluble phenolic pools. J Exp Bot 57 (2006) 1399-1411
61. Oraby H., Venkatesh B., Dale B., Ahmad R., Ransom C., Oehmke J., and Sticklen M. Enhanced conversion of plant biomass into glucose using transgenic rice-produced endoglucanase for cellulosic ethanol. Transgenic Res 16 (2007) 739-749
62. Montalvo-Rodriguez R., Haseltine C., Huess-LaRossa K., Clemente T., Soto J., Staswick P., and Blum P. Autohydrolysis of plant polysaccharides using transgenic hyperthermophilic enzymes. Biotechnol Bioeng 70 (2000) 151-159
63. Fujita Y., Takahashi S., Ueda M., Tanaka A., Okada H., Morikawa Y., Kawaguchi T., Arai M., Fukuda H., and Kondo A. Direct and efficient production of ethanol from cellulosic material with a yeast strain displaying cellulolytic enzymes. Appl Environ Microbiol 68 (2002) 5136-5141
64. Hasona A., Kim Y., Healy F.G., Ingram L.O., and Shanmugam K.T. Pyruvate formate lyase and acetate kinase are essential for anaerobic growth of Escherichia coli on xylose. J Bacteriol 186 (2004) 7593-7600
65. Datar R., Huang J., Maness P.-C., Mohagheghi A., Czernik S., and Chornet E. Hydrogen production from the fermentation of corn stover biomass pretreated with a steam-explosion process. Int J Hydrogen Energy 32 (2007) 932-939
66. Stephanopoulos G. Challenges in engineering microbes for biofuels production. Science 315 (2007) 801-804
67. Himmel M.E., Ding S.Y., Johnson D.K., Adney W.S., Nimlos M.R., Brady J.W., and Foust T.D. Biomass recalcitrance: engineering plants and enzymes for biofuels production. Science 315 (2007) 804-807
68. Pharkya P., Burgard A.P., and Maranas C.D. OptStrain: a computational framework for redesign of microbial production systems. Genome Res 14 (2004) 2367-2376
69. Nielsen J., and Jewett M.C. Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae. FEMS Yeast Res (2007)
70. Takors R., Bathe B., Rieping M., Hans S., Kelle R., and Huthmacher K. Systems biology for industrial strains and fermentation processes-example: amino acids. J Biotechnol 129 (2007) 181-190
71. Park J.H., Lee K.H., Kim T.Y., and Lee S.Y. Metabolic engineering of Escherichia coli for the production of l-valine based on transcriptome analysis and in silico gene knockout simulation. Proc Natl Acad Sci U S A 104 (2007) 7797-7802
72. Oh Y.K., Palsson B.O., Park S.M., Schilling C.H., and Mahadevan R. Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J Biol Chem 282 (2007) 28791-28799
73. Oh Y.K., Kim H.J., Park S., Kim M.S., and Ryu D.D.Y. Metabolic-flux analysis of hydrogen production pathway in Citrobacter amalonaticus Y19. Int J Hydrogen Energy 33 (2008) 1471-1482
74. Becker S.A., Feist A.M., Mo M.L., Hannum G., Palsson B.O., and Herrgard M.J. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2 (2007) 727-738
75. Klamt S., Saez-Rodriguez J., and Gilles E.D. Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst Biol 1 (2007) 2
76. Feist A.M., Henry C.S., Reed J.L., Krummenacker M., Joyce A.R., Karp P.D., Broadbelt L.J., Hatzimanikatis V., and Palsson B.O. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3 (2007) 121
77. Henry C.S., Broadbelt L.J., and Hatzimanikatis V. Thermodynamics-based metabolic flux analysis. Biophys J 92 (2007) 1792-1805
78. Schuetz R., Kuepfer L., and Sauer U. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol 3 (2007) 119
79. Alam K.Y., and Clark D.P. Anaerobic fermentation balance of Escherichia coli as observed by in vivo nuclear magnetic resonance spectroscopy. J Bacteriol 171 (1989) 6213-6217
80. Reed J.L., Vo T.D., Schilling C.H., and Palsson B.O. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 4 (2003) R54
81. Fong S.S., and Palsson B.O. Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet 36 (2004) 1056-1058