Industrial Systems Biology of Saccharomyces cerevisiae Enables Novel Succinic Acid Cell Factory

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Otero, José Manuel ^a,b,d   Cimini, Donatella ^c   Patil, Kiran R ^b,e   Poulsen, Simon G ^b   Olsson, Lisbeth ^a,b   Nielsen, Jens ^a,b  

^a CHALMERS UNIVERSITY OF TECHNOLOGY   (Sweden)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^c SECOND UNIVERSITY OF NAPLES   (Italy)

^d MERCK RESEARCH LABORATORIES   (United States)

^e EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

SUCCINATE DEHYDROGENASE; SUCCINIC ACID; TRANSCRIPTOME;

ARTICLE; BACTERIAL STRAIN; BIOMASS; BIOMASS CONVERSION; CARBON METABOLISM; CATALYSIS; CONTROLLED STUDY; GENE OVEREXPRESSION; GENE TARGETING; GROWTH RATE; METABOLIC ENGINEERING; MOLECULAR EVOLUTION; NONHUMAN; OXIDATIVE PHOSPHORYLATION; PROTON TRANSPORT; SACCHAROMYCES CEREVISIAE; SYSTEMS BIOLOGY;

ALDEHYDE-LYASES; BIOMASS; CITRIC ACID CYCLE; DIRECTED MOLECULAR EVOLUTION; FERMENTATION; INDUSTRIAL MICROBIOLOGY; METABOLIC ENGINEERING; MODELS, GENETIC; MUTATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SUCCINIC ACID; SYSTEMS BIOLOGY; TRANSAMINASES; TRANSCRIPTOME;

EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 84872655172     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0054144     Document Type: Article

References (36)

1. Otero JM, Panagiotou G, Olsson L, (2007) Fueling Industrial Biotechnology Through Bioethanol. Adv Biochem Eng Biotechnol 108: 1-40.
2. Nielsen J, (2001) Metabolic engineering. Appl Microbiol Biotechnol 55(3): 263-283.
3. Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, et al. (2001) Metabolic modeling of microbial strains in silico. Trends Biochem Sci 26(3): 179-186.
4. Nielsen J, Jewett MC, (2008) Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae. FEMS Yeast Res 8(1): 122-131.
5. Bro C, Regenberg B, Förster J, Nielsen J, (2005) In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Metabolic Engineering 8(2): 102-111.
6. Edwards JS, Ibarra RU, Palsson BØ, (2001) In silico predictions of Eschericia coli metabolic capabilities are consistent with experimental data. Nature Biotechnology 19(2): 125-130.
7. McKinlay JB, Vieille C, Zeikus JG, (2007) Prospects for a bio-based succinate industry. Appl Microbiol Biotechnol 76(4): 727-740.
8. Wilke T, Vorlop KD, (2004) Industrial bioconversion of renewable resources as an alternative to conventional chemistry. Appl Microbiol Biotechnol 66(2): 131-142.
9. Zeikus JG, Jain MK, Elankovan P, (1999) Biotechnology of succinic acid production and markets for dervied industrial products. Appl Microbiol Biotechnol 51: 545-552.
10. Song H, Lee SY, (2006) Production of succinic acid by bacterial fermentation. Enzy Microb Techn 39(3): 352-361.
11. Jantama K, Haupt MJ, Svoronos SA, Zhang X, Moore JC, et al. (2008) Combining metabolic engineering and metabolic evolution to develop nonrecombinant strains of Escherichia coli C that produce succinate and malate. Biotechnol Bioeng 99(5): 1140-1153.
12. Lee PC, Lee SY, Hong SH, Chang HN, (2002) Isolation and characterization of a new succinic acid-producing bacterium, Mannheimia succiniciproducens MBEL55E, from bovine rumen. Appl Microbiol Biotechnol 58(5): 663-668.
13. Sauer M, Porro D, Mattanovich D, Braunduardi P, (2008) Microbial production of organic acids: expanding the markets. Trends Biotechnol 26(2): 100-108.
14. Adrio JL, Deman AL, (2006) Genetic improvement of processes yielding microbial products. FEMS Microbiol Rev 30(2): 187-214.
15. Lynd LR, Wyman CE, Gerngross TU, (1999) Biocommodity Engineering. Biotecnol Prog 15(5): 777-793.
16. Patil KR, Rocha I, Förster J, Nielsen J, (2005) Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 6: 308-319.
17. Cimini D, Patil KR, Schiraldi C, Nielsen J, (2009) Global transcritional response of Saccharomyces cerevisiae to the deletion of SDH3. BMC Systems Biology 3(1): 17-28.
18. Aliverdieva DA, Mamaev DV, Lagutina LS, Scholtz KF, (2006) Specific features of changes in levels of endogenous respiration substrates in Saccharomyces cerevisiae cells at low temperature. Biochemistry (Moscow) 71(1): 39-45.
19. Regenberg B, Grotkjær T, Winther O, Fausbøll A, Akesson M, et al. (2006) Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in Saccharomyces cerevisiae. Genome Biol 7(11): R107-119.
20. Castrillo JI, Zeef LA, Hoyle DC, Zhang N, Hayes A, et al. (2007) Growth control of the eukaryote cell: a systems biology study in yeast. J Biol 6(2): 4-28.
21. Fazio A, Jewett MC, Daran-Lapujade P, Mustacchi R, Usaite R, et al. (2008) Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: A three factor design. BMC Genomics 9: 341-354.
22. Paley SM, Karp PD, (2006) The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Research 34(13): 3771-3778.
23. Fisk DG, Ball CA, Dolinski K, Engel SR, Hong EL, et al. (2006) Saccharomyces cerevisiae S288C genome annotation: a working hypothesis. Yeast 23(12): 857-865.
24. Förster J, Famili I, Fu P, Palsson BØ, Nielsen J, (2003) Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 13(2): 244-253.
25. Duarte NC, Harrgård MJ, Palsson BØ, (2004) Reconstruction and validation of Saccaromyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 14(7): 1298-1309.
26. Nookaew I, Jewett MC, Meechai A, Thammarongtham C, Laoteng K, et al. (2008) The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism. BMC Systems Biology 7(2): 71-85.
27. Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, et al. (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology 26 (10): 1155-1160.
28. Wattanachaisaereekul S, Lantz AE, Nielsen ML, Nielsen J, (2008) Production of the polyketide 6-MSA in yeast engineered for increased malonyl-CoA supply. Metab Eng 10(5): 246-254.
29. Zelle RM, de Hulster E, van Winden WA, de Waard P, Dijkema C, et al. (2008) Malic acid production by Saccharomyces cerevisiae: Engineering of pyruvate carboxylation, oxaloacetate reduction, and malate export. Appl Environ Microbiol 74(9): 2766-2777.
30. van Dijken JP, Bauer J, Brambilla L, Duboc P, Francois JM, et al. (2000) An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme and Microbial Technology 26(9-10): 706-714.
31. Eredeniz N, Mortensen UH, Rothstein R, (1997) Cloning-free PCR-based allele replacement methods. Genome Res 7: 1174-1183.
32. Gietz RD, Woods RA, (2002) Transformation of yeast by lithium acetate/single-straded carrier DNA/polyethylene glycol method. Methods Enzymol 350: 87-96.
33. Christianson TW, Sikorski RS, Dante M, Shero JH, Hieter P, (1992) Multifunctional yeast high-copy-number shuttle vectors. Gen 110(1): 119-122.
34. Verudyn C, Postma E, Scheffers WA, van Dijken JP, (1992) Effect of benzoic acid on metabolic fluxes in yeasts: a continuous culture stody on the regulation of respiration and alcoholic fermentation. Yeast 8: 501-517.
35. Smyth GK (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3, 1(3).
36. Smyth GK (2005) Limma: linear models for microarray data. In Bioinformatics and Computational Biology Solutions using R and Bioconductor, Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W (eds.), 397-420, New York: Springer.