Construction of microbial cell factories for industrial bioprocesses

Journal of Chemical Technology and Biotechnology

Volumn 87, Issue 4, 2012, Pages 445-450

  Sauer, Michael ^a,b   Mattanovich, Diethard ^a,b  

^a UNIVERSITY OF NATURAL RESOURCES AND LIFE SCIENCES   (Austria)

^b AUSTRIAN CENTRE OF INDUSTRIAL BIOTECHNOLOGY   (Austria)

Author keywords

Industrial microbiology; Metabolic engineering; Metabolic modelling; Strain improvement; Synthetic biology; Systems biology

Indexed keywords

CELLULAR NETWORK; ENVIRONMENTAL ISSUES; ENZYMATIC REACTION; FACTORY DESIGN; GAINING INSIGHTS; INDUSTRIAL BIOPROCESSES; METABOLIC MODELLING; MICROBIAL CELLS; MICROBIAL PROCESS; PETROLEUM RESOURCES; SINGLECELL ANALYSIS; STRAIN IMPROVEMENT; STRUCTURAL BIOLOGY; SUPPLY INDUSTRY; SYNTHETIC BIOLOGY; SYSTEMS BIOLOGY; TIME SYSTEMS;

CELLS; CELLULAR NEURAL NETWORKS; DESIGN; INDUSTRIAL MICROBIOLOGY; INDUSTRY; METABOLIC ENGINEERING; PETROLEUM DEPOSITS;

CYTOLOGY;

ALCOHOL; ARTEMISINIC ACID; PETROLEUM; XYLOSE;

AMINO ACID SYNTHESIS; ARTEMISIA ANNUA; ARTICLE; BIOCATALYST; BIOMASS; BIOTECHNOLOGY; BIOTRANSFORMATION; CATALYSIS; CELL STRUCTURE; CORYNEBACTERIUM GLUTAMICUM; DOWN REGULATION; ENZYME MECHANISM; ESCHERICHIA COLI; FERMENTATION; FUNGAL STRAIN; GENOME ANALYSIS; HIGH THROUGHPUT SCREENING; KLEBSIELLA PNEUMONIAE; LACTOCOCCUS LACTIS; MATHEMATICAL MODEL; METABOLIC ENGINEERING; MOLECULAR MODEL; MUTAGENESIS; NONHUMAN; PHENOTYPE; PICHIA STIPITIS; SACCHAROMYCES CEREVISIAE; SCREENING; SEQUENCE ANALYSIS; STEADY STATE; STOICHIOMETRY; SYNTHETIC BIOLOGY; SYSTEMS BIOLOGY;

EID: 84858279030     PISSN: 02682575     EISSN: 10974660     Source Type: Journal    
DOI: 10.1002/jctb.3711     Document Type: Article

References (63)

1. Du J, Shao Z and Zhao H, Engineering microbial factories for synthesis of value-added products. J Ind Microbiol Biotechnol 38: 873-890 (2011).
2. Bailey JE, Toward a science of metabolic engineering. Science 252: 1668-1675 (1991).
3. Stephanopoulos G and Sinskey AJ, Metabolic engineering-methodologies and future prospects. Trends Biotechnol 11: 392-396 (1993).
4. Stephanopoulos G, Metabolic engineering. Curr Opin Biotechnol 5: 196-200 (1994).
5. Nowrousian M, Next-generation sequencing techniques for eukaryotic microorganisms: sequencing-based solutions to biological problems. Eukaryot Cell 9: 1300-1310 (2010).
6. van Vliet AH, Next generation sequencing of microbial transcriptomes: challenges and opportunities. FEMS Microbiol Lett 302: 1-7 (2010).
7. Smith DR, Quinlan AR, Peckham HE, Makowsky K, Tao W, Woolf B et al, Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res 18: 1638-1642 (2008).
8. Chen Z, Wilmanns M and Zeng AP, Structural synthetic biotechnology: from molecular structure to predictable design for industrial strain development. Trends Biotechnol 28: 534-542 (2010).
9. Nakamura CE and Whited GM, Metabolic engineering for the microbial production of 1, 3-propanediol. Current Opin Biotechnol 14: 454-459 (2003).
10. Zeng AP and Biebl H, Bulk chemicals from biotechnology: the case of 1, 3-propanediol production and the new trends. Adv Biochem Eng Biotechnol 74: 239-259 (2002).
11. Sauer M, Marx H and Mattanovich D, Microbial production of 1, 3-propanediol. Recent Pat Biotechnol 2: 191-197 (2008).
12. Ro DK, Paradise EM, Ouellet M, Fisher KJ, Newman KL, Ndungu JM et al, Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440: 940-943 (2006).
13. Becker JV, Armstrong GO, van der Merwe MJ, Lambrechts MG, Vivier MA and Pretorius IS, Metabolic engineering of Saccharomyces cerevisiae for the synthesis of the wine-related antioxidant resveratrol. FEMS Yeast Res 4: 79-85 (2003).
14. Katz M, Smits HP, Forster J and Nielsen JB, Metabolically engineered cells for the production of resveratrol or an oligomeric or glycosidically-bound derivative thereof. US Patent Application 0286844 A1 (2008).
15. Beekwilder J, Wolswinkel R, Jonker H, Hall R, de Vos CH and Bovy A, Production of resveratrol in recombinant microorganisms. Appl Environ Microbiol 72: 5670-5672 (2006).
16. Lee SY, Kim HU, Park JH, Park JM and Kim TY, Metabolic engineering of microorganisms: general strategies and drug production. Drug Discov Today 14: 78-88 (2009).
17. Schlitt T and Brazma A, Current approaches to gene regulatory network modelling. BMC Bioinformatics 8: S9 (2007).
18. Greller LD and Somogyi R, Reverse engineers map the molecular switching yards. Trends Biotechnol 20: 445-447 (2002).
19. Kim HU, Kim TY and Lee SY, Metabolic flux analysis and metabolic engineering of microorganisms. Mol Biosyst 4: 113-120 (2008).
20. Price ND, Papin JA, Schilling CH and Palsson BO, Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol 21: 162-169 (2003).
21. Price ND, Reed JL and Palsson BO, Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2: 886-897 (2004).
22. Burgard AP, Pharkya P and Maranas CD, Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 84: 647-657 (2003).
23. Pharkya P and Maranas CD, An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab Eng 8: 1-13 (2006).
24. Pharkya P, Burgard AP and Maranas CD, OptStrain: a computational framework for redesign of microbial production systems. Genome Res 14: 2367-2376 (2004).
25. Blank LM and Kuepfer L, Metabolic flux distributions: genetic information, computational predictions, and experimental validation. Appl Microbiol Biotechnol 86: 1243-1255 (2010).
26. Teusink B, Wiersma A, Molenaar D, Francke C, de Vos WM, Siezen RJ et al, Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J Biol Chem 281: 40041-40048 (2006).
27. Lee SJ, Song H and Lee SY, Genome-based metabolic engineering of Mannheimia succiniciproducens for succinic acid production. Appl Environ Microbiol 72: 1939-1948 (2006).
28. 13C-labeling of proteinogenic amino acids. An efficient analytical tool to investigate intermediary metabolism. Eur J Biochem 232: 433-448 (1995).
29. 13C-based flux analysis. Mol Syst Biol 2: 62 (2006).
30. Becker J, Klopprogge C, Herold A, Zelder O, Bolten CJ and Wittmann C, Metabolic flux engineering of L-lysine production in Corynebacterium glutamicum-over expression and modification of G6P dehydrogenase. J Biotechnol 132: 99-109 (2007).
31. Becker J, Klopprogge C, Schröder H and Wittmann C, Metabolic engineering of the tricarboxylic acid cycle for improved lysine production by Corynebacterium glutamicum. Appl Environ Microbiol 75: 7866-869 (2009).
32. Becker J, Zelder O, Häfner S, Schröder H and Wittmann C, From zero to hero -design-based systems metabolic engineering of Corynebacterium glutamicum for L-lysine production. Metab Eng 13: 159-168 (2011).
33. Kohlstedt M, Becker J and Wittmann C, Metabolic fluxes and beyond-systems biology understanding and engineering of microbial metabolism. Appl Microbiol Biotechnol 88: 1065-1075 (2010).
34. Park JH, Lee SY, Kim TY and Kim HU, Application of systems biology for bioprocess development. Trends Biotechnol 26: 404-412 (2008).
35. Na D, Kim TY and Lee SY, Construction and optimization of synthetic pathways in metabolic engineering. Curr Opin Microbiol 13: 363-370 (2010).
36. Mattanovich D, Gasser B, Hohenblum H and Sauer M, Stress in recombinant protein producing yeasts. J Biotechnol 113: 121-135 (2004).
37. Nicolaou SA, Gaida SM and Papoutsakis ET, A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: from biofuels and chemicals, to biocatalysis and bioremediation. Metab Eng 12: 307-331 (2010).
38. Branduardi P, Fossati T, Sauer M, Pagani R, Mattanovich D and Porro D, Biosynthesis of vitamin C by yeast leads to increased stress resistance. PLoS One 2: e1092 (2007).
39. Abbott D, Suir E, Duong G, de Hulster E, Pronk J and van Maris A, Catalase overexpression reduces lactic acid-induced oxidative stress in Saccharomyces cerevisiae. Appl Environ Microbiol 75: 2320-2325 (2009).
40. Zhang W, Li F and Nie L, Integrating multiple 'omics' analysis for microbial biology: application and methodologies. Microbiology 156: 287-301 (2010).
41. Askenazi M, Driggers EM, Holtzman DA, Norman TC, Iverson S, Zimmer DP et al, Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains. Nat Biotechnol 21: 150-156 (2003).
42. Cai L, Friedman N and Xie XS, Stochastic protein expression in individual cells at the single molecule level. Nature 440: 358-362 (2006).
43. Kaern M, Elston TC, Blake WJ and Collins JJ, Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 6: 451-464 (2005).
44. Dong D, Shao X, Deng N and Zhang Z, Gene expression variations are predictive for stochastic noise. Nucleic Acids Res 39: 403-413 (2011).
45. Schmid A, Kortmann H, Dittrich PS and Blank LM, Chemical and biological single cell analysis. Curr Opin Biotechnol 21: 12-20 (2010).
46. Kortmann H, Blank LM and Schmid A, Single cell analytics: an overview. Adv Biochem Eng Biotechnol 124: 99-122 (2011).
47. Borland LM, Kottegoda S, Phillips KS and Allbritton NL, Chemical analysis of single cells. Annu Rev Anal Chem (Palo Alto Calif) 1: 191-227 (2008).
48. Wang D and Bodovitz S, Single cell analysis: the new frontier in 'omics'. Trends Biotechnol 28: 281-290 (2010).
49. Beltrao P, Kiel C and Serrano L, Structures in systems biology. Curr Opin Struct Biol 17: 378-384 (2007).
50. McArthur GH and Fong SS, Toward engineering synthetic microbial metabolism. J Biomed Biotechnol 2010: 459760 (2010).
51. Röthlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J et al, Kemp elimination catalysts by computational enzyme design. Nature 453: 190-195 (2008).
52. Khersonsky O, Röthlisberger D, Dym O, Albeck S, Jackson CJ, Baker D et al, Evolutionary optimization of computationally designed enzymes: kemp eliminases of the KE07 series. J Mol Biol 396: 1025-1042 (2010).
53. Mainguet SE and Liao JC, Bioengineering of microorganisms for C3 to C5 alcohols production. Biotechnol J 5: 1297-1308 (2010).
54. Atsumi S, Hanai T and Liao JC, Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451: 86-89 (2008).
55. Zhang K, Sawaya MR, Eisenberg DS and Liao JC, Expanding metabolism for biosynthesis of nonnatural alcohols. Proc Natl Acad Sci USA 105: 20653-20658 (2008).
56. Strickland D, Moffat K and Sosnick TR, Light-activated DNA binding in a designed allosteric protein. Proc Natl Acad Sci USA 105: 10709-10714 (2008).
57. Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV et al, Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol 27: 753-759 (2009).
58. Valli M, Sauer M, Branduardi P, Borth N, Porro D and Mattanovich D, Improvement of lactic acid production in Saccharomyces cerevisiae by cell sorting for high intracellular pH. Appl Environ Microbiol 72: 5492-5499 (2006).
59. Sauer U, Evolutionary engineering of industrially important microbial phenotypes. Adv Biochem Eng Biotechnol 73: 129-169 (2001).
60. Wisselink HW, Toirkens MJ, Wu Q, Pronk JT and van Maris AJ, Novel evolutionary engineering approach for accelerated utilization of glucose, xylose, and arabinose mixtures by engineered Saccharomyces cerevisiae strains. Appl Environ Microbiol 75: 907-914 (2009).
61. Hong KK, Vongsangnak W, Vemuri GN and Nielsen J, Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis. Proc Natl Acad Sci USA 108: 12179-12184 (2011).
62. Conrad TM, Lewis NE and Palsson BO, Microbial laboratory evolution in the era of genome-scale science. Mol Syst Biol 7: 509 (2011).
63. Sauer M, Porro D, Mattanovich D and Branduardi P, Microbial production of organic acids: expanding the markets. Trends Biotechnol 26: 100-108 (2008).