123
Views
17
CrossRef citations to date
0
Altmetric
Review

Systems biology approaches for the microbial production of biofuels

&
Pages 291-310 | Published online: 09 Apr 2014

Bibliography

  • Energy Information Association. Annual Energy Outlook 2009 with Projections to 2030. US Department of Energy (2009).
  • Rath BB. Harvesting alternate energies from our planet. J. Mineral, Metals Materials Soc.61(4),73–78 (2009).
  • McKendry P. Energy production from biomass (part 2): conversion technologies. Bioresource Technol.83,47–54 (2002).
  • Yang S-T. Bioprocessing For Value-Added Products From Renewable Resources: New Technologies And Applications. Elsevier BV, UK (2007).
  • Rosenberg JN, Oyler GA, Wilkinson L, Betenbaugh MJ. A green light for engineered algae: redirecting metabolism to fuel a biotechnology revolution. Curr. Opin. Biotechnol.19(5),430–436 (2008).
  • Smith AM. Prospects for increasing starch and sucrose yields for bioethanol production. Plant J.54(4),546–558 (2008).
  • Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res.36,D475–D479 (2008).
  • Gray KA, Zhao LS, Emptage M. Bioethanol. Curr. Opin. Chem. Biol.10(2),141–146 (2006).
  • Demirbas A. The importance of bioethanol and biodiesel from biomass. Energy Sources B Economics Plann. Policy3(2),177–185 (2008).
  • Nielsen DR, Leonard E, Yoon SH, Tseng HC, Yuan C, Prather KLJ. Engineering alternative butanol production platforms in heterologous bacteria. Metabol. Eng.11(4–5),262–273 (2009).
  • Atsumi S, Cann AF, Connor MR et al. Metabolic engineering of Escherichia coli for 1-butanol production. Metabol. Eng.10(6),305–311 (2008).
  • Shen CR, Liao JC. Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways. Metabol. Eng.10(6),312–320 (2008).
  • Withers ST, Gottlieb SS, Lieu B, Newman JD, Keasling JD. Identification of isopentenol biosynthetic genes from Bacillus subtilis by a screening method based on isoprenoid precursor toxicity. Appl. Environ. Microbiol.73(19),6277–6283 (2007).
  • Kalscheuer R, Stolting T, Steinbuchel A. Microdiesel: Escherichia coli engineered for fuel production. Microbiol. SGM, 152,2529–2536 (2006).
  • Sauer U. Evolutionary engineering of industrially important microbial phenotypes. Adv. Biochem. Eng. Biotechnol.73,129–169 (2001).
  • Kern A, Tilley E, Hunter IS, Legisa M, Glieder A. Engineering primary metabolic pathways of industrial micro-organisms. J. Biotechnol.129(1),6–29 (2007).
  • Lee SK, Chou H, Ham TS, Lee TS, Keasling JD. Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels. Curr. Opin. Biotechnol.19(6),556–563 (2008).
  • Mukhopadhyay A, Redding AM, Rutherford BJ, Keasling JD. Importance of systems biology in engineering microbes for biofuel production. Curr. Opin. Biotechnol.19(3),228–234 (2008).
  • Lee SY, Lee DY, Kim TY. Systems biotechnology for strain improvement. Trends Biotechnol.23(7),349–358 (2005).
  • Hieter P, Boguski M. Functional genomics: it’s all how you read it. Science278(5338),601–602 (1997).
  • Ideker T, Galitski T, Hood L. A new approach to decoding life: systems biology. Ann. Rev. Genomics Hum. Genet.2,343–372 (2001).
  • Ishii N, Nakahigashi K, Baba T et al. Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science316(5824),593–597 (2007).
  • Koide T, Pang W, Baliga N. The role of predictive modelling in rationally re-engineering biological systems. Nat. Rev. Microbiol.7,297–305 (2009).
  • Stephanopoulos G, Alper H, Moxley J. Exploiting biological complexity for strain improvement through systems biology. Nat. Biotechnol.22(10),1261–1267 (2004).
  • Zhang SL, Ye BC, Chu J, Zhuang YP, Guo MJ. From multi-scale methodology to systems biology: to integrate strain improvement and fermentation optimization. J. Chem. Technol. Biotechnol.81(5),734–745 (2006).
  • Schmeisser C, Steele H, Streit WR. Metagenomics, biotechnology with non-culturable microbes. Appl. Microbiol. Biotechnol.75(5),955–962 (2007).
  • Smith DR, Quinlan AR, Peckham HE et al. Rapid whole-genome mutational profiling using next-generation sequencing technologies. Genome Res.18(10),1638–1642 (2008).
  • Lin J, Qian J. Systems biology approach to integrative comparative genomics. Expert Rev. Proteomics4(1),107–119 (2007).
  • Dharmadi Y, Gonzalez R. DNA microarrays: Experimental issues, data analysis, and application to bacterial systems. Biotechnol. Prog.20(5),1309–1324 (2004).
  • Lockhart DJ, Winzeler EA. Genomics, gene expression and DNA arrays. Nature405(6788),827–836 (2000).
  • Graham RL, Graham C, McMullan G. Microbial proteomics: a mass spectrometry primer for biologists. Microbial Cell Factories6,26 (2007).
  • Watt SA, Patschkowski T, Kalinowski J, Niehaus K. Qualitative and quantitative proteomics by two-dimensional gel electrophoresis, peptide mass fingerprint and a chemically-coded affinity tag (CCAT). J. Biotechnol.106(2–3),287–300 (2003).
  • Gevaert K, Van Damme P, Ghesquiere B et al.A la carte proteomics with an emphasis on gel-free techniques. Proteomics7(16),2698–2718 (2007).
  • Raamsdonk L, Teusink B, Broadhurst D et al. A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat. Biotechnol.19,45–50 (2001).
  • Buchholz A, Hurlebaus J, Wandrey C, Takors R. Metabolomics: quantification of intracellular metabolite dynamics. Biomol. Eng.19(1),5–15 (2002).
  • Kell DB. Metabolomics and systems biology: making sense of the soup. Curr. Opin. Microbiol.7(3),296–307 (2004).
  • Tang YJ, Martin HG, Myers S, Rodriguez S, Baidoo EEK, Keasling JD. Advances in analysis of microbial metabolic fluxes via C-13 isotopic labeling. Mass Spec. Rev.28(2),362–375 (2009).
  • Varma A, Palsson BO. Metabolic flux balancing – basic concepts, scientific and practical use. Biotechnol.12(10),994–998 (1994).
  • Suthers PF, Burgard AP, Dasika MS et al. Metabolic flux elucidation for large-scale models using C-13 labeled isotopes. Metabol. Eng.9(5–6),387–405 (2007).
  • Joyce AR, Palsson BO. The model organism as a system: integrating ‘omics’ data sets. Nat. Rev. Mol. Cell Biol.7(3),198–210 (2006).
  • Ishii N, Robert M, Nakayama Y, Kanai A, Tomita M. Toward large-scale modeling of the microbial cell for computer simulation. J. Biotechnol.281–294 (2004).
  • Vertes AA, Inui M, Yukawa H. Manipulating corynebacteria, from individual genes to chromosomes. Appl. Environ. Microbiol.71(12),7633–7642 (2005).
  • Tsuchida T, Momose H. Improvement of an l-leucine-producing mutant of Brevibacterium lactofermentum 2256 by genetically desensitizing it to α-acetohydroxy acid synthetase. Appl. Environ. Microbiol.51(5),1024–1027 (1986).
  • Sahm H, Eggeling L, Eikmanns B, Kramer R. Construction of l-lysine-, L-threonine, or L-isoleucine-overproducing strains of Corynebacterium glutamicum. Integration Biol. Eng. Sci.782,25–39 (1996).
  • Chotani G, Dodge T, Hsu A et al. The commercial production of chemicals using pathway engineering. Biochim. Biophys. Acta Protein Structure Molecular Enzymology1543(2),434–455 (2000).
  • Vemuri GN, Aristidou AA. Metabolic engineering in the omics era: elucidating and modulating regulatory networks. Microbiol. Mol. Biol. Rev.69(2),197–216 (2005).
  • Bailey JE. Toward a science of metabolic engineering. Science252(5013),1668–1675 (1991).
  • Atsumi S, Liao JC. Metabolic engineering for advanced biofuels production from Escherichia coli. Curr. Opin. Biotechnol.19(5),414–419 (2008).
  • Liu J, Weng Z, Wang Y, Chao H, Zongwan M. Metabolic engineering based on systems biology for chemicals production. Front. Biol. China4(3),260–265 (2009).
  • Ladygina N, Dedyukhina EG, Vainshtein MB. A review on microbial synthesis of hydrocarbons. Process Biochem.41(5),1001–1014 (2006).
  • Liao JC, Higashide W. Metabolic engineering of next-generation biofuels. Chem. Eng. Progress104(8),S19–S23 (2008).
  • Stephanopoulos G. Challenges in engineering microbes for biofuels production. Science315(5813),801–804 (2007).
  • Otero JM, Panagiotou G, Olsson L. Fueling industrial biotechnology growth with bioethanol. In: Biofuels. Springer-Verlag Berlin, Berlin, Germany, 1–40 (2007).
  • Stephanopoulos G, Stafford DE. Metabolic engineering: a new frontier of chemical reaction engineering. Chem. Eng. Sci.57(14),2595–2602 (2002).
  • Bailey JE, Sburlati A, Hatzimanikatis V, Lee K, Renner WA, Tsai PS. Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes. Biotechnol. Bioeng.52(1),109–121 (1996).
  • Bengtsson O, Jeppsson M, Sonderegger M et al. Identification of common traits in improved xylose-growing Saccharomyces cerevisiae for inverse metabolic engineering. Yeast25(11),835–847 (2008).
  • Jin YS, Alper H, Yang YT, Stephanopoulos G. Improvement of xylose uptake and ethanol production in recombinant Saccharomyces cerevisiae through an inverse metabolic engineering approach. Appl. Environ. Microbiol.71(12),8249–8256 (2005).
  • Jantama K, Haupt MJ, Svoronos SA et al. 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 (2008).
  • Park JH, Lee SY. Towards systems metabolic engineering of microorganisms for amino acid production. Curr. Opin. Biotechnol.19(5),454–460 (2008).
  • Koffas M, Stephanopoulos G. Strain improvement by metabolic engineering: lysine production as a case study for systems biology. Curr. Opin. Biotechnol.16(3),361–366 (2005).
  • Senger RS, Papoutsakis ET. Genome-scale model for Clostridium acetobutylicum: Part I. Metabolic network resolution and analysis. Biotechnol. Bioeng.101(5),1036–1052 (2008).
  • van Ommen B. Nutrigenomics: exploiting systems biology in the nutrition and health arenas. Nutrition20(1),4–8 (2004).
  • Shi S, Chen T, Zhang Z, Chen X, Zhao X. Transcriptome analysis guided metabolic engineering of Bacillus subtilis for riboflavin production. Metabol. Eng.11,243–252 (2009).
  • Lubke C, Boidol W, Petri T. Analysis and optimization of recombinant protein production in Escherichia coli using the inducible Pho-A promoter of the Escherichia coli alkaline-phosphatase. Enz. Microb. Technol.17(10),923–928 (1995).
  • Sommer B, Friehs K, Flaschel E, Reck M, Stahl F, Scheper T. Extracellular production and affinity purification of recombinant proteins with Escherichia coli using the versatility of the maltose binding protein. J. Biotechnol.140(3–4),194–202 (2009).
  • Patnaik R. Engineering complex phenotypes in industrial strains. Biotechnol. Prog.24(1),38–47 (2008).
  • Warner JR, Patnaik R, Gill RT. Genomics enabled approaches in strain engineering. Curr. Opin. Microbiol.12(3),223–230 (2009).
  • Zhang YX, Perry K, Vinci VA, Powell K, Stemmer WPC, del Cardayre SB. Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature415(6872),644–646 (2002).
  • Lynch MD, Warnecke T, Gill RT. SCALEs: multiscale analysis of library enrichment. Nat. Methods4(1),87–93 (2007).
  • Alper H, Stephanopoulos G. Global transcription machinery engineering: a new approach for improving cellular phenotype. Metabol. Eng.9(3),258–267 (2007).
  • Tyo KE, Alper HS, Stephanopoulos GN. Expanding the metabolic engineering toolbox: more options to engineer cells. Trends Biotechnol.25(3),132–137 (2007).
  • Herring CD, Raghunathan A, Honisch C et al. Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat. Genet.38(12),1406–1412 (2006).
  • Shi DJ, Wang CL, Wang KM. Genome shuffling to improve thermotolerance, ethanol tolerance and ethanol productivity of Saccharomyces cerevisiae. J. Industrial Microbiol. Biotechnol.36(1),139–147 (2009).
  • Bonomo J, Lynch MD, Warnecke T, Price JV, Gill RT. Genome-scale analysis of anti-metabolite directed strain engineering. Metabol. Eng.10(2),109–120 (2008).
  • Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G. Engineering yeast transcription machinery for improved ethanol tolerance and production. Science314(5805),1565–1568 (2006).
  • Yomano LP, York SW, Ingram LO. Isolation and characterization of ethanol-tolerant mutants of Escherichia coli KO11 for fuel ethanol production. J. Industrial Microbiol. Biotechnol.20(2),132–138 (1998).
  • Gonzalez R, Tao H, Shanmugam KT, York SW, Ingram LO. Global gene expression differences associated with changes in glycolytic flux and growth rate in Escherichia coli during the fermentation of glucose and xylose. Biotechnol. Prog.18(1),6–20 (2002).
  • Gonzalez R, Tao H, Purvis JE, York SW, Shanmugam KT, Ingram LO. Gene array-based identification of changes that contribute to ethanol tolerance in ethanologenic Escherichia coli: comparison of KO11 (Parent) to LY01 (resistant mutant). Biotechnol. Prog.19(2),612–623 (2003).
  • Atsumi S, Hanai T, Liao JC. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature451(7174),86–89. (2008).
  • Park JH, Lee KH, Kim TY, Lee SY. 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. USA104(19),7797–7802 (2007).
  • Paredes CJ, Alsaker KV, Papoutsakis ET. A comparative genomic view of clostridial sporulation and physiology. Nat. Rev. Microbiol.3(12),969–978 (2005).
  • Harris LM, Desai RP, Welker NE, Papoutsakis ET. Characterization of recombinant strains of the Clostridium acetobutylicum butyrate kinase inactivation mutant: Need for new phenomenological models for solventogenesis and butanol inhibition? Biotechnol. Bioeng.67(1),1–11 (2000).
  • Clark SW, Bennett GN, Rudolph FB. Isolation and characterization of mutants of Clostridium acetobutylicum ATCC-824 deficient in acetoacetyl – coenzyme A -acetate butyrate – coenzyme A – transferase (EC 2.8.3.9) and in other solvent pathway enzymes. Appl. Environ. Microbiol.55(4),970–976 (1989).
  • Dinh TN, Nagahisa K, Yoshikawa K, Hirasawa T, Furusawa C, Shimizu H. Analysis of adaptation to high ethanol concentration in Saccharomyces cerevisiae using DNA microarray. Bioprocess Biosystems Engineering32(5),681–688 (2009).
  • Tomas CA, Welker NE, Papoutsakis ET. Overexpression of groESL in Clostridium acetobutylicum results in increased solvent production and tolerance, prolonged metabolism, and changes in the cell’s transcriptional program. Appl. Environ. Microbiol.69(8),4951–4965 (2003).
  • Tomas CA, Beamish J, Papoutsakis ET. Transcriptional analysis of butanol stress and tolerance in Clostridium acetobutylicum. J. Bacteriol.186(7),2006–2018 (2004).
  • Bensmail H, Haoudi A. Data mining in genomics and proteomics. J. Biomed. Biotechnol.(2),63–64 (2005).
  • Van den Bulcke T, Lemmens K, Van de Peer Y, Marchal K. Inferring transcriptional networks by mining ‘Omics’ data. Curr. Bioinformatics1(3),301–313 (2006).
  • Wang RS, Wang Y, Zhang XS, Chen L. Inferring transcriptional regulatory networks from high-throughput data. Bioinformatics23(22),3056–3064 (2007).
  • Chen DC, Liu ZQ, Ma XB, Hua D. Selecting genes by test statistics. J. Biomed. Biotechnol.2,132–138 (2005).
  • Rollins DK, Zhai DM, Joe AL, Guidarelli JW, Murarka A, Gonzalez R. A novel data mining method to identify assay-specific signatures in functional genomic studies. BMC Bioinformatics7,377 (2006).
  • Brynildsen MP, Liao JC. An integrated network approach identifies the isobutanol response network of Escherichia coli. Mol. Systems Biol.5,277 (2009).
  • Westergaard SL, Oliveira AP, Bro C, Olsson L, Nielsen J. A systems biology approach to study glucose repression in the yeast Saccharomyces cerevisiae. Biotechnol. Bioeng.96(1),134–145 (2007).
  • Sullivan L, Bennett GN. Proteome analysis and comparison of Clostridium acetobutylicum ATCC 824 and Spo0A strain variants. J. Industrial Microbiol. Biotechnol.33(4),298–308 (2006).
  • Cheng JS, Qiao B, Yuan YJ. Comparative proteome analysis of robust Saccharomyces cerevisiae insights into industrial continuous and batch fermentation. Appl. Microbiol. Biotechnol.81(2),327–338 (2008).
  • Kolkman A, Olsthoorn MMA, Heeremans CEM, Heck AJR, Slijper M. Comparative proteome analysis of Saccharomyces cerevisiae grown in chemostat cultures limited for glucose or ethanol. Mol. Cell. Proteomics4(1),1–11 (2005).
  • Cheng JS, Zhou X, Ding MZ, Yuan YJ. Proteomic insights into adaptive responses of Saccharomyces cerevisiae to the repeated vacuum fermentation. Appl. Microbiol. Biotechnol.83(5),909–923 (2009).
  • Kedar P, Colah R, Shimizu K. Proteomic investigation on the pyk-F gene knockout Escherichia coli for aromatic amino acid production. Enzyme Microbial Technol.41(4),455–465 (2007).
  • Keasling JD, Chou H. Metabolic engineering delivers next-generation biofuels. Nat. Biotechnol.26(3),298–299 (2008).
  • Williams TI, Combs JC, Lynn BC, Strobel HJ. Proteomic profile changes in membranes of ethanol-tolerant Clostridium thermocellum. Appl. Microbiol. Biotechnol.74(2),422–432 (2007).
  • Soga T, Ohashi Y, Ueno Y, Naraoka H, Tomita M, Nishioka T. Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. J. Proteome Res.2(5),488–494 (2003).
  • Mashego MR, Jansen MLA, Vinke JL, van Gulik WM, Heijnen JJ. Changes in the metabolome of Saccharomyces cerevisiae associated with evolution in aerobic glucose-limited chemostats. Fems Yeast Research, 5(4–5),419–430 (2005).
  • Burlingame AL, Carr SA. Mass Spectrometry of Bacterial Lipoosaccharides. Humana Press, NJ, USA, 570 (2007).
  • Mashego MR, Gulik WM, Heijnen JJ. Metabolome dynamic responses of Saccharomyces cerevisiae to simultaneous rapid perturbations in external electron acceptor and electron donor. Fems Yeast Res.7(1),48–66 (2007).
  • Ding MZ, Cheng JS, Xiao WH, Qiao B, Yuan YJ. Comparative metabolomic analysis on industrial continuous and batch ethanol fermentation processes by GC-TOF-MS. Metabolomics5(2),229–238 (2009).
  • Fernie AR, Trethewey RN, Krotzky AJ, Willmitzer L. Innovation – metabolite profiling: from diagnostics to systems biology. Nat. Rev. Mol. Cell Biol.5(9),763–769 (2004).
  • Berrios-Rivera SJ, Bennett GN, San KY. The effect of increasing NADH availability on the redistribution of metabolic fluxes in Escherichia coli chemostat cultures. Metabol. Eng.4(3),230–237 (2002).
  • Amore R, Kotter P, Kuster C, Ciriacy M, Hollenberg CP. Cloning and expression in Saccharomyces cerevisiae of the NAD(P)H-dependent xylose reductase-encoding gene (xyl1) from the xylose-assimilating yeast Pichia stipitis. Gene109(1),89–97 (1991).
  • Fonseca C, Neves AR, Antunes AMM et al. Use of in vivo C-13 nuclear magnetic resonance spectroscopy to elucidate L-arabinose metabolism in yeasts. Appl. Environ. Microbiol.74(6),1845–1855 (2008).
  • Grotkjaer T, Christakopoulos P, Nielsen J, Olsson L. Comparative metabolic network analysis of two xylose fermenting recombinant Saccharomyces cerevisiae strains. Metabol. Eng.7(5–6),437–444 (2005).
  • Iwatani S, Yamada Y, Usuda Y. Metabolic flux analysis in biotechnology processes. Biotechnol. Lett.30(5),791–799 (2008).
  • Kotter P, Ciriacy M. Xylose fermentation by Saccharomyces cerevisiae. Appl. Microbiol. Biotechnol.38(6),776–783 (1993).
  • Raghevendran V, Gombert AK, Christensen B, Kotter P, Nielsen J. Phenotypic characterization of glucose repression mutants of Saccharomyces cerevisiae usinge experiments with C-13-labelled glucose. Yeast21(9),769–779 (2004).
  • Fortman JL, Chhabra S, Mukhopadhyay A et al. Biofuel alternatives to ethanol: pumping the microbial well. Trends Biotechnol.26(7),375–381 (2008).
  • Martin VJJ, Pitera DJ, Withers ST, Newman JD, Keasling JD. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol.21(7),796–802 (2003).
  • Borden JR, Papoutsakis ET. Dynamics of genomic-library enrichment and identification of solvent tolerance genes for Clostridium acetobutylicum. Appl. Environ. Microbiol.73(9),3061–3068 (2007).
  • Alsaker KV, Papoutsakis ET. Transcriptional program of early sporulation and stationary-phase events in Clostridium acetobutylicum. J. Bacteriol.187(20),7103–7118 (2005).
  • Schaffer S, Isci N, Zickner B, Durre P. Changes in protein synthesis and identification of proteins specifically induced during solventogenesis in Clostridium acetobutylicum. Electrophoresis23(1),110–121 (2002).
  • Seo JS, Chong HY, Park HS et al. The genome sequence of the ethanologenic bacterium Zymomonas mobilis ZM4. Nat. Biotechnol.23(1),63–68 (2005).
  • Yang SH, Tschaplinski TJ, Engle NL et al. Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations. BMC Genomics10,34 (2009).
  • Matsushika A, Inoue H, Kodaki T, Sawayama S. Ethanol production from xylose in engineered Saccharomyces cerevisiae strains: current state and perspectives. Appl. Microbiol. Biotechnol.84(1),37–53 (2009).
  • Salusjarvi L, Kankainen M, Soliymani R, Pitkanen JP, Penttila M, Ruohonen L. Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae. Microbial Cell Factories4(7),18 (2008).
  • Ideker T, Thorsson V, Ranish JA et al. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science292(5518),929–934 (2001).
  • Price ND, Papin JA, Schilling CH, Palsson BO. Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol.21(4),162–169 (2003).
  • Raman K, Chandra N. Flux balance analysis of biological systems: applications and challenges. Briefings Bioinformatics10(4),435–449 (2009).
  • Harris LM, Blank L, Desai RP, Welker NE, Papoutsakis ET. Fermentation characterization and flux analysis of recombinant strains of Clostridium acetobutylicum with an inactivated solR gene. J. Industrial Microbiol. Biotechnol.27(5),322–328 (2001).
  • Lee J, Yun H, Feist AM, Palsson BO, Lee SY. Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Appl. Microbiol. Biotechnol.80(5),849–862 (2008).
  • Senger RS, Papoutsakis ET. Genome-scale model for Clostridium acetobutylicum: Part II. Development of specific proton flux states and numerically determined sub-systems. Biotechnol. Bioeng.101(5),1053–1071 (2008).
  • Burgard AP, Pharkya P, Maranas CD. OptKnock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng.84(6),647–657 (2003).
  • Hjersted JL, Henson MA, Mahadevan R. Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture. Biotechnol. Bioeng.97(5),1190–1204 (2007).
  • Lloyd CM, Lawson JR, Hunter PJ, Nielsen PF. The CellML model repository. Bioinformatics24(18),2122–2123 (2008).
  • Tomita M, Hashimoto K, Takahashi K et al. E-CELL: software environment for whole-cell simulation. Bioinformatics15(1),72–84 (1999).
  • Stromback L, Lambrix P. Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX. Bioinformatics21(24),4401–4407 (2005).
  • Snoep JL, Olivier BG. JWS online cellular systems modelling and microbiology. Microbiol. SGM149,3045–3047 (2003).
  • Rizzi M, Baltes M, Theobald U, Reuss M. In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae 2. Mathematical model. Biotechnol. Bioeng.55(4),592–608 (1997).
  • Gupta P, Lee KH. Genomics and proteomics in process development: opportunities and challenges. Trends Biotechnol.25(7),324–330 (2007).
  • Park JH, Lee SY, Kim TY, Kim HU. Application of systems biology for bioprocess development. Trends Biotechnol.26(8),404–412 (2008).
  • Hanai T, Atsumi S, Liao JC. Engineered synthetic pathway for isopropanol production in Escherichia coli. Appl. Environ. Microbiol.73(24),7814–7818 (2007).
  • Dellomonaco C, Rivera C, Campbell P, Gonzalez R. Synthetic respiro-fermentative metabolism for the conversion of bio-oils to fuels and chemicals: a new biorefinery paradigm. Appl. Environ. Microbiol. (2010)(In Press).
  • Dellomonaco C, Fava F, Gonzalez R. The path to next generation biofuels: Successes and challenges in the era of synthetic biology. Microbial Cell Factories9(3) (2010).
  • Wei P, Li Z, He P, Lin Y, Jiang N. Genome shuffling in the ethanologenic yeast Candida krusei to improve acetic acid tolerance. Biotechnol. Appl. Biochem.49,113–120 (2008).
  • Kocabaş P, Çalik P, Çalik G, Őzdamar T. Microarray studies in Bacillus subtilis. Biotechnol. J.4(7),1012–1027 (2009).
  • Shilling O, Frick O, Herzberg C et al. Transcriptional and metabolic responses of Bacillus subtilis to the availability of organic acids: transcription regulation is important but not sufficient to account for metabolic adaptation. Appl. Environ. Microbiol.73(2),499–507 (2007).
  • Alsaker KV, Spitzer TR, Papoutsakis ET. Transcriptional analysis of spo0A overexpression in Clostridium acetobutylicum and its effect on the cell’s response to butanol stress. J. Bacteriol.186(7),1959–1971 (2004).
  • Tummala SB, Junne SG, Paredes CJ, Papoutsakis ET. Transcriptional analysis of product-concentration driven changes in cellular programs of recombinant Clostridium acetobutylicum strains. Biotechnol. Bioeng.84(7),842–854 (2003).
  • Shi Z, Blaschek HP. Transcriptional qnalysis of Clostridium beijerinckii NCIMB 8052 and the hyper-butanol-producing mutant BA101 during the shift from acidogenesis to solventogenesis. Appl. Environ. Microbiol.74(24),7709–7714 (2008).
  • Miller EN, Jarboe LR, Yomano LP, York SW, Shanmugam KT, Ingram LO. Silencing of NADPH-dependent oxidoreductase genes (yqhD and dkgA) in furfural-resistant ethanologenic Escherichia coli. Appl. Environ. Microbiol.75(13),4315–4323 (2009).
  • Miller EN, Jarboe LR, Turner PC et al. Furfural inhibits growth by limiting sulfur assimilation in ethanologenic Escherichia coli strain LY180. Appl. Environ. Microbiol.75(19),6132–6141 (2009).
  • Daran-Lapujade P, Jansen MLA, Daran JM, van Gulik W, de Winde JH, Pronk JT. Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae – a chemostat culture study. J. Biol. Chem.279(10),9125–9138 (2004).
  • Karhumaa K, Pahlman AK, Hahn-Hagerdal B, Levander F, Gorwa-Grauslund MF. Proteome analysis of the xylose-fermenting mutant yeast strain TMB 3400. Yeast26(7),371–382 (2009).
  • Lin FM, Qiao B, Yuan YJ. Comparative proteomic analysis of tolerance and adaptation of ethanologenic Saccharomyces cerevisiae to furfural, a lignocellulosic inhibitory compound. Appl. Environ. Microbiol.75(11),3765–3776 (2009).
  • Peng LF, Shimizu K. Effect of fadR gene knockout on the metabolism of Escherichia coli based on analyses of protein expressions, enzyme activities and intracellular metabolite concentrations. Enz. Microbial Technol.38(3–4),512–520 (2006).
  • Sauer U, Lasko DR, Fiaux J et al. Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism. J. Bacteriol.181(21),6679–6688 (1999).
  • Pitkanen JP, Aristidou A, Salusjarvi L, Ruohonen L, Penttila M. Metabolic flux analysis of xylose metabolism in recombinant Saccharomyces cerevisiae using continuous culture. Metabol. Eng.5(1),16–31 (2003).
  • Kashiwagi A, Sakurai T, Tsuru S, Ying BW, Mori K, Yomo T. Construction of Escherichia coli gene expression level perturbation collection. Metabol. Eng.11(1),56–63 (2009).
  • Kizer L, Pitera DJ, Pfleger BF, Keasling JD. Application of functional genomics to pathway optimization for increased isoprenoid production. Appl. Environ. Microbiol.74(10),3229–3241 (2008).
  • Lee KH, Park JH, Kim TY, Kim HU, Lee SY. Systems metabolic engineering of Escherichia coli for L-threonine production. Mol. Systems Biol.3,149 (2007).
  • Salusjarvi L, Pitkanen JP, Aristidou A, Ruohonen L, Penttila M. Transcription analysis of recombinant Saccharomyces cerevisiae reveals novel responses to xylose. Appl. Biochem. Biotechnol.128(3),237–261 (2006).
  • Dharmadi Y, Gonzalez R. Elementary network reconstruction: A framework for the analysis of regulatory networks in biological systems. J. Theor. Biol. DOI: 10.1016/j.jtbi.2009.12.007 (2009) (Epub ahead of print).
  • Edwards JS, Ibarra RU, Palsson BO. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol.19(2),125–130 (2001).
  • Reed JL, Vo TD, Schilling CH, Palsson BO. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol.4(9),R54 (2003).
  • Forster J, Famili I, Fu P, Palsson BO, Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res.13(2),244–253 (2003).
  • Duarte NC, Palsson BO, Fu PC. Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae. BMC Genomics5,63 (2004).
  • Altintas MM, Eddy CK, Zhang M, McMillan JD, Kompala DS. Kinetic modeling to optimize pentose fermentation in Zymomonas mobilis. Biotechnol. Bioeng.94(2),273–295 (2006).

▪ Website

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.