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Systems Biology of Industrial Microorganisms

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Biosystems Engineering I

Part of the book series: Advances in Biochemical Engineering / Biotechnology ((ABE,volume 120))

Abstract

The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.

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References

  1. Bailey JE (1991) Science 252:1668–1675

    Article  CAS  Google Scholar 

  2. Nielsen J (2001) Appl Microbiol Biotechnol 55:263–283

    Article  CAS  Google Scholar 

  3. Stephanopoulos G, Aristidou A, Nielsen J (1998) Metabolic engineering: principles and methodologies. Academic, San Diego

    Google Scholar 

  4. Jewett MC, Hofmann G, Nielsen J (2006) Curr Opin Biotechnol 17:191–197

    Article  CAS  Google Scholar 

  5. Raab RM, Tyo K, Stephanopoulos G (2005) Adv Biochem Eng Biotechnol 100:1–17

    CAS  Google Scholar 

  6. Sanford K, Soucaille P, Whited G et al (2002) Curr Opin Microbiol 5:318–322

    Article  CAS  Google Scholar 

  7. Otero JM, Olsson L, Nielsen J (2007) Genet Eng News 27:28–31

    Google Scholar 

  8. Chotani G, Dodge T, Hsu A et al (2000) Biochim Biophys Acta 1543:434–455

    Article  CAS  Google Scholar 

  9. Gavrilescu M, Chisti Y (2005) Biotechnol Adv 23:471–499

    Article  CAS  Google Scholar 

  10. van Berkel R (2000) Cleaner production for process industries. Plenary Lecture, Chemeca, Perth, WA

    Google Scholar 

  11. Energy Information Administration. Available at http://www.eia.doe.gov/. Accessed 15 Jan 2009

  12. McKinsey (2003) Available at http://www.mckinsey.com/mgi/publications/turkey/index.asp. Accessed 30 Jan 2009

  13. Lee SY, Kim HU, Park JH et al (2009) Drug Discov Today 14:78–88

    Article  CAS  Google Scholar 

  14. Otero JM, Nielsen J (2009) Industrial Systems Biology. Biotechnol Bioeng 105(3): 439–460

    Google Scholar 

  15. Barnett JA (2003) Microbiology 149:557–567

    Article  CAS  Google Scholar 

  16. Hamilton SR, Davidson RC, Sethuraman N et al (2006) Science 313:1441–1443

    Article  CAS  Google Scholar 

  17. Li HJ, Sethuraman N, Stadheim TA et al (2006) Nat Biotechnol 24:210–215

    Article  CAS  Google Scholar 

  18. Karaffa L, Kubicek CP (2003) Appl Microbiol Biotechnol 61:189–196

    CAS  Google Scholar 

  19. Davies RW (1994) Prog Ind Microbiol 29:527–560

    CAS  Google Scholar 

  20. Blattner FR, Plunkett G, Bloch CA et al (1997) Science 277:1453–1474

    Article  CAS  Google Scholar 

  21. Galagan JE, Calvo SE, Cuomo C et al (2005) Nature 438:1105–1115

    Article  CAS  Google Scholar 

  22. Goffeau A, Barrell BG, Bussey H et al (1996) Science 274:546–567

    Article  CAS  Google Scholar 

  23. Kunst F, Ogasawara N, Moszer I et al (1997) Nature 390:249–256

    Article  CAS  Google Scholar 

  24. Machida M, Asai K, Sano M et al (2005) Nature 438:1157–1161

    Article  Google Scholar 

  25. Martinez D, Berka RM, Henrissat B et al (2008) Nat Biotechnol 26:553–560

    Article  CAS  Google Scholar 

  26. Nierman WC, Pain A, Anderson MJ et al (2005) Nature 438:1151–1156

    Article  CAS  Google Scholar 

  27. Pel HJ, de Winde JH, Archer DB et al (2007) Nat Biotechnol 25:221–231

    Article  Google Scholar 

  28. Nielsen J, Jewett MC (2006) Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae. In: 25th International specialized symposium on Yeasts (ISSY25), Blackwell, Espoo, Finland

    Google Scholar 

  29. Sanger F, Air GM, Barrell BG et al (1977) Nature 265:687–695

    Article  CAS  Google Scholar 

  30. Smith HO, Tomb JF, Dougherty BA et al (1995) Science 269:538–540

    Article  CAS  Google Scholar 

  31. Galagan JE, Calvo SE, Borkovich KA et al (2003) Nature 422:859–868

    Article  CAS  Google Scholar 

  32. Shendure J, Mitra RD, Varma C et al (2004) Nat Rev Genet 5:335–344

    Article  CAS  Google Scholar 

  33. Collins FS, Morgan M, Patrinos A (2003) Science 300:286–290

    Article  CAS  Google Scholar 

  34. Shendure J, Ji HL (2008) Nat Biotechnol 26:1135–1145

    Article  CAS  Google Scholar 

  35. Frazier ME, Johnson GM, Thomassen DG et al (2003) Science 300:290–293

    Article  CAS  Google Scholar 

  36. Gabig M, Wegrzyn G (2001) Acta Biochim Pol 48:615–622

    CAS  Google Scholar 

  37. Affymetrix. Available at http://www.affymetrix.com/index.affx. Accessed 20 Jan 2009

  38. NimbleGen. Available at http://www.nimblegen.com/. Accessed 20 Jan 2009

  39. Agilent Technologies. Available at http://www.chem.agilent.com/en-US/products/instruments/dnamicroarrays/pages/default.aspx. Accessed 20 Jan 2009

  40. Fermlab. Available at http://www.fermlab.com/motechinfo.html. Accessed 20 Jan 2009

  41. Febit. Available at http://www.febit.com/go/en/. Accessed 20 Jan 2009

  42. Jewett MC, Oliveira AP, Patil KR et al (2005) Biotechnol Bioprocess Eng 10:385–399

    Article  CAS  Google Scholar 

  43. Jarmer H, Berka R, Knudsen S et al (2002) FEMS Microbiol Lett 206:197–200

    Article  CAS  Google Scholar 

  44. Gene Expression Omnibus Database. Available at http://www.ncbi.nlm.nih.gov/geo/. Accessed 20 Jan 2009

  45. Array Express Database. Available at http://www.ebi.ac.uk/microarray-as/ae/. Accessed 20 Jan 2009

  46. Roberts GG, Hudson AP (2006) Mol Genet Genomics 276:170–186

    Article  CAS  Google Scholar 

  47. Usaite R, Patil KR, Grotkjaer T et al (2006) Appl Environ Microbiol 72:6194–6203

    Article  CAS  Google Scholar 

  48. Borodina I, Siebring J, Zhang J et al (2008) J Biol Chem 283:25186–25199

    Article  CAS  Google Scholar 

  49. Yuan XL, van der Kaaij RM, van den Hondel C et al (2008) Mol Genet Genomics 279:545–561

    Article  CAS  Google Scholar 

  50. Vongsangnak W, Salazar M, Hansen K, Nielsen J (2009) Genome-wide analysis of maltose utilization and regulation in aspergilli. Microbiology 155:3893–3902

    Google Scholar 

  51. Askenazi M, Driggers EM, Holtzman DA et al (2003) Nat Biotechnol 21:150–156

    Article  CAS  Google Scholar 

  52. Anderson NL, Anderson NG (1998) Electrophoresis 19:1853–1861

    Article  CAS  Google Scholar 

  53. Joyce AR, Palsson BO (2006) Nat Rev Mol Cell Biol 7:198–210

    Article  CAS  Google Scholar 

  54. Gygi SP, Rist B, Gerber SA et al (1999) Nat Biotechnol 17:994–999

    Article  CAS  Google Scholar 

  55. Zhu H, Bilgin M, Bangham R et al (2001) Science 293:2101–2105

    Article  CAS  Google Scholar 

  56. Bader GD, Hogue CWV (2002) Nat Biotechnol 20:991–997

    Article  CAS  Google Scholar 

  57. Auerbach D, Thaminy S, Hottiger MO, Stagljar I (2002) The post-genomic era of interactive proteomics: Facts and perspectives. Proteomics 2:611–623

    Google Scholar 

  58. Ghaemmaghami S, Huh W, Bower K et al (2003) Nature 425:737–741

    Article  CAS  Google Scholar 

  59. Kniemeyer O, Lessing F, Scheibner O et al (2006) Curr Genet 49:178–189

    Article  CAS  Google Scholar 

  60. Mueller LN, Brusniak MY, Mani DR et al (2008) J Proteome Res 7:51–61

    Article  CAS  Google Scholar 

  61. Nesvizhskii AI, Vitek O, Aebersold R (2007) Nat Methods 4:787–797

    Article  CAS  Google Scholar 

  62. Taylor CF, Binz PA, Aebersold R et al (2008) Nat Biotechnol 26:860–861

    Article  CAS  Google Scholar 

  63. Gupta N, Benhamida J, Bhargava V et al (2008) Genome Res 18:1133–1142

    Article  CAS  Google Scholar 

  64. Mapelli V, Olsson L, Nielsen J (2008) Trends Biotechnol 26:490–497

    Article  CAS  Google Scholar 

  65. Tweeddale H, Notley-McRobb L, Ferenci T (1998) J Bacteriol 180:5109–5116

    CAS  Google Scholar 

  66. Oliver SG, Winson MK, Kell DB et al (1998) Trends Biotechnol 16:373–378

    Article  CAS  Google Scholar 

  67. Dunn WB, Bailey NJC, Johnson HE (2005) Analyst 130:606–625

    Article  CAS  Google Scholar 

  68. Werner E, Heilier JF, Ducruix C et al (2008) J Chromatogr B 871:143–163

    Article  CAS  Google Scholar 

  69. Raamsdonk LM, Teusink B, Broadhurst D et al (2001) Nat Biotechnol 19:45–50

    Article  CAS  Google Scholar 

  70. Soga T, Ueno Y, Naraoka H et al (2002) Anal Chem 74:2233–2239

    Article  CAS  Google Scholar 

  71. Soga T, Kakazu Y, Robert M et al (2004) Electrophoresis 25:1964–1972

    Article  CAS  Google Scholar 

  72. Kaderbhai NN, Broadhurst DI, Ellis DI et al (2003) Comp Funct Genomics 4:376–391

    Article  CAS  Google Scholar 

  73. Maharjan RP, Seeto S, Ferenci T (2007) J Bacteriol 189:2350–2358

    Article  CAS  Google Scholar 

  74. Allen J, Davey HM, Broadhurst D et al (2003) Nat Biotechnol 21:692–696

    Article  CAS  Google Scholar 

  75. Mas S, Villas-Boas SG, Hansen ME et al (2007) Biotechnol Bioeng 96:1014–1022

    Article  CAS  Google Scholar 

  76. Kouskoumvekaki I, Yang ZY, Jonsdottir SO et al (2008) BMC Bioinformatics 9:59

    Article  CAS  Google Scholar 

  77. Smedsgaard J, Nielsen J (2005) J Exp Bot 56:273–286

    Article  CAS  Google Scholar 

  78. Pope GA, MacKenzie DA, Defemez M et al (2007) Yeast 24:667–679

    Article  CAS  Google Scholar 

  79. Howell KS, Cozzolino D, Bartowsky EJ et al (2006) FEMS Yeast Res 6:91–101

    Article  CAS  Google Scholar 

  80. Sumner LW, Amberg A, Barrett D et al (2007) Metabolomics 3:211–221

    Article  CAS  Google Scholar 

  81. BIGG Database. Available at www.bigg.ucsd.edu/. Accessed 20 Jan 2009

  82. BioCyc Database. Available at www.biocyc.org/. Accessed 20 Jan 2009

  83. MSlib Database. Available at www.ualberta.ca/∼gjones/mslib.htm. Accessed 20 Jan 2009

  84. NIST Database. Available at www.nist.gov/srd/nist1a.htm. Accessed 20 Jan 2009

  85. Metlin Database. Available at www.metlin.scripps.edu. Accessed 20 Jan 2009

  86. HMDB Database. Available at www.hmdb.ca/extrIndex.htm. Accessed 20 Jan 2009

  87. Nielsen J (2003) J Bacteriol 185:7031–7035

    Article  CAS  Google Scholar 

  88. Sauer U (2004) Curr Opin Biotechnol 15:58–63

    Article  CAS  Google Scholar 

  89. Daran-Lapujade P, Rossell S, van Gulik WM et al (2007) Proc Natl Acad Sci USA 104:15753–15758

    Article  CAS  Google Scholar 

  90. ter Kuile BH, Westerhoff HV (2001) FEBS Lett 500:169–171

    Article  Google Scholar 

  91. Sauer U (2006) Mol Syst Biol 2:62

    Article  Google Scholar 

  92. Marx A, de Graaf AA, Wiechert W et al (1996) Biotechnol Bioeng 49:111–129

    Article  CAS  Google Scholar 

  93. Sauer U, Hatzimanikatis V, Bailey JE et al (1997) Nat Biotechnol 15:448–452

    Article  CAS  Google Scholar 

  94. Gombert AK, dos Santos MM, Christensen B et al (2001) J Bacteriol 183:1441–1451

    Article  CAS  Google Scholar 

  95. Klapa MI, Quackenbush J (2003) Biotechnol Bioeng 84:739–742

    Article  CAS  Google Scholar 

  96. Wiechert W, de Graaf AA (1997) Biotechnol Bioeng 55:101–117

    Article  CAS  Google Scholar 

  97. Wiechert W, Siefke C, de Graaf AA et al (1997) Biotechnol Bioeng 55:118–135

    Article  CAS  Google Scholar 

  98. Wiechert W, Mollney M, Isermann N et al (1999) Biotechnol Bioeng 66:69–85

    Article  CAS  Google Scholar 

  99. van Winden WA, Heijnen JJ, Verheijen PJT (2002) Biotechnol Bioeng 80:731–745

    Article  CAS  Google Scholar 

  100. Christensen B, Gombert AK, Nielsen J (2002) Eur J Biochem 269:2795–2800

    Article  CAS  Google Scholar 

  101. Chen KC, Csikasz-Nagy A, Gyorffy B et al (2000) Mol Biol Cell 11:369–391

    CAS  Google Scholar 

  102. Klipp E (2007) Yeast 24:943–959

    Article  CAS  Google Scholar 

  103. Borodina I, Nielsen J (2005) Curr Opin Biotechnol 16:350–355

    Article  CAS  Google Scholar 

  104. Ibarra RU, Edwards JS, Palsson BO (2002) Nature 420:186–189

    Article  CAS  Google Scholar 

  105. Edwards JS, Covert M, Palsson B (2002) Environ Microbiol 4:133–140

    Article  Google Scholar 

  106. Famili I, Forster J, Nielson J et al (2003) Proc Natl Acad Sci USA 100:13134–13139

    Article  CAS  Google Scholar 

  107. Forster J, Famili I, Fu P et al (2003) Genome Res 13:244–253

    Article  CAS  Google Scholar 

  108. Bonarius HPJ, Schmid G, Tramper J (1997) Trends Biotechnol 15:308–314

    Article  CAS  Google Scholar 

  109. Stephanopoulos G (1998) Biotechnol Bioeng 58:119–120

    Article  CAS  Google Scholar 

  110. Patil KR, Akesson M, Nielsen J (2004) Curr Opin Biotechnol 15:64–69

    Article  CAS  Google Scholar 

  111. Schilling CH, Covert MW, Famili I et al (2002) J Bacteriol 184:4582–4593

    Article  CAS  Google Scholar 

  112. Edwards JS, Ibarra RU, Palsson BO (2001) Nat Biotechnol 19:125–130

    Article  CAS  Google Scholar 

  113. Covert MW, Palsson BO (2002) J Biol Chem 277:28058–28064

    Article  CAS  Google Scholar 

  114. Breitling R, Vitkup D, Barrett MP (2008) Nat Rev Microbiol 6:156–161

    Article  CAS  Google Scholar 

  115. Henry CS, Broadbelt LJ, Hatzimanikatis V (2007) Biophys J 92:1792–1805

    Article  CAS  Google Scholar 

  116. Jamshidi N, Palsson BO (2008) Mol Syst Biol 4

    Google Scholar 

  117. Hinnen A, Meyhack B, Heim J (1989) Biotechnology 13:193–213

    CAS  Google Scholar 

  118. Mustacchi R, Hohmann S, Nielsen J (2006) Yeast 23:227–238

    Article  CAS  Google Scholar 

  119. Petranovic D, Nielsen J (2008) Trends Biotechnol 26:584–590

    Article  CAS  Google Scholar 

  120. Vemuri GN, Aristidou A (2005) Microbiol Mol Biol Rev 69:197–216

    Article  CAS  Google Scholar 

  121. Romanos MA, Scorer CA, Clare JJ (1992) Yeast 8:423–488

    Article  CAS  Google Scholar 

  122. Giaever G, Chu AM, Ni L et al (2002) Nature 418:387–391

    Article  CAS  Google Scholar 

  123. Chigira Y, Oka T, Okajima T et al (2008) Glycobiology 18:303–314

    Article  CAS  Google Scholar 

  124. Hamilton SR, Gerngross TU (2007) Curr Opin Biotechnol 18:387–392

    Article  CAS  Google Scholar 

  125. Gasser B, Mattanovich D (2007) Biotechnol Lett 29:201–212

    Article  CAS  Google Scholar 

  126. Parekh S, Vinci VA, Strobel RJ (2000) Appl Microbiol Biotechnol 54:287–301

    Article  CAS  Google Scholar 

  127. Rowlands RT (1984) Enzyme Microb Technol 6:3–10

    Article  CAS  Google Scholar 

  128. Attfield PV, Bell PJL (2003) Genetics and classical genetic manipulation of industrial yeasts. In: Functional Genetics of Industrial Yeasts. de Winde JH, ed, Topics in Current Genetics, (S Hohmann, Series Ed), 2, pp 17–55. Springer-Verlag, Heidelberg and New York

    Google Scholar 

  129. Weuster-Botz D, Hekmat D, Puskeiler R et al (2007) Adv Biochem Eng Biotechnol 105:205–247

    CAS  Google Scholar 

  130. Patnaik R, Louie S, Gavrilovic V et al (2002) Nat Biotechnol 20:707–712

    Article  CAS  Google Scholar 

  131. Spencer JFT, Spencerd DM, Reynolds N (1988) J Basic Microbiol 28:321–333

    Article  CAS  Google Scholar 

  132. Demain AL, Solomon NA (1986) Manual of industrial microbiology and biotechnology. American Society for Biotechnology, Washington, DC

    Google Scholar 

  133. Lindegren CC, Lindegren G (1943) Proc Natl Acad Sci USA 29:306–308

    Article  CAS  Google Scholar 

  134. Romano P, Soli MG, Suzzi G et al (1985) Appl Environ Microbiol 50:1064–1067

    CAS  Google Scholar 

  135. Urano N, Sato M, Sahara H et al (1993) J Biotechnol 28:249–261

    Article  CAS  Google Scholar 

  136. Higgins VJ, Bell PJL, Dawes IW et al (2001) Appl Environ Microbiol 67:4346–4348

    Article  CAS  Google Scholar 

  137. Angelov AI, Karadjov GI, Roshkova ZG (1996) Food Res Int 29:235–239

    Article  CAS  Google Scholar 

  138. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

    Google Scholar 

  139. van Dijck P, Gorwa MF, Lemaire K et al (2000) Int J Food Microbiol 55:187–192

    Article  Google Scholar 

  140. Dequin S (2001) Appl Microbiol Biotechnol 56:577–588

    Article  CAS  Google Scholar 

  141. Donalies UEB, Nguyen HTT, Stahl U et al (2008) Adv Biochem Eng Biotechnol 111:67–98

    CAS  Google Scholar 

  142. Klein CJL, Olsson L, Nielsen J (1998) Microbiology 144:13–14

    Article  CAS  Google Scholar 

  143. Klein CJL, Olsson L, Ronnow B et al (1996) Appl Environ Microbiol 62:4441–4449

    CAS  Google Scholar 

  144. Olsson L, Larsen ME, Ronnow B et al (1997) Appl Environ Microbiol 63:2366–2371

    CAS  Google Scholar 

  145. Liljeström-Suominen PL, Joutsjoki V, Korhola M (1988) Appl Environ Microbiol 54:245–249

    Google Scholar 

  146. Rønnow B, Olsson L, Nielsen J et al (1999) J Biotechnol 72:213–228

    Article  Google Scholar 

  147. Bidard F, Blondin B, Dequin S et al (1994) Curr Genet 25:196–201

    Article  CAS  Google Scholar 

  148. Riou C, Nicaud JM, Barre P et al (1997) Yeast 13:903–915

    Article  CAS  Google Scholar 

  149. Verstrepen KJ, Bauer F, Michiels C et al (1999) Eur Brew Conv Mon 28:30

    Google Scholar 

  150. Londesborough J (1995) US Patent 5,422,254

    Google Scholar 

  151. Lewis JG, Learmonth RP, Attfield PV et al (1997) J Ind Microbiol Biotechnol 18:30–36

    Article  CAS  Google Scholar 

  152. Auras R, Harte B, Selke S (2004) Macromol Biosci 4:835–864

    Article  CAS  Google Scholar 

  153. John RP, Nampoothiri KM, Pandey A (2007) Appl Microbiol Biotechnol 74:524–534

    Article  CAS  Google Scholar 

  154. Datta R, Henry M (2006) J Chem Technol Biotechnol 81:1119–1129

    Article  CAS  Google Scholar 

  155. Singh SK, Ahmed SU, Pandey A (2006) Proc Biochem 41:991–1000

    Article  CAS  Google Scholar 

  156. Porro D, Brambilla L, Ranzi BM et al (1995) Biotechnol Prog 11:294–298

    Article  CAS  Google Scholar 

  157. Hohmann S (1991) J Bacteriol 173:7963–7969

    CAS  Google Scholar 

  158. Porro D, Bianchi MM, Brambilla L et al (1999) Appl Environ Microbiol 65:4211–4215

    CAS  Google Scholar 

  159. van Maris AJA, Winkler AA, Porro D et al (2004) Appl Environ Microbiol 70:2898–2905

    Article  CAS  Google Scholar 

  160. Andrade RP, Casal M (2001) Fungal Genet Biol 32:105–111

    Article  CAS  Google Scholar 

  161. Branduardi P, Sauer M, De Gioia L et al (2006) Microb Cell Fact 5

    Google Scholar 

  162. Porro D, Bianchi MM, Ranzi BM et al (1999) Yeast strains for the production of lactic acid. PCT WO 99/14335

    Google Scholar 

  163. Yamano S, Ishii T, Nakagawa M et al (1994) Biosci Biotechnol Biochem 58:1112–1114

    Article  CAS  Google Scholar 

  164. Verwaal R, Wang J, Meijnen JP et al (2007) Appl Environ Microbiol 73:4342–4350

    Article  CAS  Google Scholar 

  165. Miura Y, Kondo K, Saito T et al (1998) Appl Environ Microbiol 64:1226–1229

    CAS  Google Scholar 

  166. Polakowski T, Stahl U, Lang C (1998) Appl Microbiol Biotechnol 49:66–71

    Article  CAS  Google Scholar 

  167. Shimada H, Kondo K, Fraser PD et al (1998) Appl Environ Microbiol 64:2676–2680

    CAS  Google Scholar 

  168. Szczebara FM, Chandelier C, Villeret C et al (2003) Nat Biotechnol 21:143–149

    Article  CAS  Google Scholar 

  169. Gerngross TU (2004) Nat Biotechnol 22:1409–1414

    Article  CAS  Google Scholar 

  170. Directory of P450-containing Systems. Available at http://www.icgeb.org/∼p450srv/. Accessed 20 Jan 2009

  171. Werck-Reichhart D, Feyereisen R (2000) Genome Biol 1:rev 3003.3001–rev 3003.3009

    Article  Google Scholar 

  172. Duport C, Spagnoli R, Degryse E et al (1998) Nat Biotechnol 16:186–189

    Article  CAS  Google Scholar 

  173. Dumas B, Brocard-Masson C, Assemat-Lebrun K et al (2006) Biotechnol J 1:299–307

    Article  CAS  Google Scholar 

  174. Baker SE, Bennett JW (2008) An overview of the genus Aspergillus. In: Goldman GH, Osmani SA (eds) The Aspergilli: genomics, medical aspects, biotechnology, and research methods, 1st edn. CRC, Taylor & Francis, Boca Raton, Florida

    Google Scholar 

  175. Perrone G, Susca A, Cozzi G et al (2007) Stud Mycol 59:53–66

    Article  CAS  Google Scholar 

  176. Barbesgaard P, Heldthansen HP, Diderichsen B (1992) Appl Microbiol Biotechnol 36:569–572

    Article  CAS  Google Scholar 

  177. Schuster E, Dunn-Coleman N, Frisvad JC et al (2002) Appl Microbiol Biotechnol 59:426–435

    Article  CAS  Google Scholar 

  178. Blumenthal CZ (2004) Regul Toxicol Pharmacol 39:214–228

    Article  CAS  Google Scholar 

  179. van Dijck PWM, Selten GCM, Hempenius RA (2003) Regul Toxicol Pharmacol 38:27–35

    Article  CAS  Google Scholar 

  180. Tilburn J, Scazzocchio C, Taylor GG et al (1983) Gene 26:205–221

    Article  CAS  Google Scholar 

  181. Meyer V (2008) Biotechnol Adv 26:177–185

    Article  CAS  Google Scholar 

  182. Bird D, Bradshaw R (1997) Mol Gen Genet 255:219–225

    Article  CAS  Google Scholar 

  183. Krappmann S, Sasse C, Braus GH (2006) Eukaryot Cell 5:212–215

    Article  CAS  Google Scholar 

  184. Hua SB, Qiu MS, Chan E et al (1997) Plasmid 38:91–96

    Article  CAS  Google Scholar 

  185. Kooistra R, Hooykaas PJJ, Steensma HY (2004) Yeast 21:781–792

    Article  CAS  Google Scholar 

  186. Ninomiya Y, Suzuki K, Ishii C et al (2004) Proc Natl Acad Sci USA 101:12248–12253

    Article  CAS  Google Scholar 

  187. Takahashi T, Masuda T, Koyama Y (2006) Mol Genet Genomics 275:460–470

    Article  CAS  Google Scholar 

  188. Meyer V, Arentshorst M, El-Ghezal A et al (2007) J Biotechnol 128:770–775

    Article  CAS  Google Scholar 

  189. Ishibashi K, Suzuki K, Ando Y et al (2006) Proc Natl Acad Sci USA 103:14871–14876

    Article  CAS  Google Scholar 

  190. Mizutani O, Kudo Y, Saito A et al (2008) Fungal Genet Biol 45:878–889

    Article  CAS  Google Scholar 

  191. de Groot MJA, Bundock P, Hooykaas PJJ et al (1998) Nat Biotechnol 16:839–842

    Article  Google Scholar 

  192. Michielse CB, Arentshorst M, Ram AFJ et al (2005) Fungal Genet Biol 42:9–19

    Article  CAS  Google Scholar 

  193. Ruiz-Diez B (2002) J Appl Microbiol 92:189–195

    Article  CAS  Google Scholar 

  194. Nielsen J (1998) Curr Opin Microbiol 1:330–336

    Article  CAS  Google Scholar 

  195. van Dijck PWM (2008) The importance of Aspergilli and regulatory aspects of Aspergillus nomenclature in biotechnology. In: Varga J, Samson RA (eds) Aspergillus in the genomic era. Wageningen Academic, Wageningen, The Netherlands

    Google Scholar 

  196. Chotani GK, Dodge TC, Gaertner AL et al (2007) Industrial biotechnology: discovery to delivery. In: Kent JA (ed) Kent and Riegel’s handbook of industrial chemistry and biotechnology, 11th edn. Springer-Verlag, New York

    Google Scholar 

  197. Currie JN (1917) J Biol Chem 31:15–37

    CAS  Google Scholar 

  198. Machida M, Yamada O, Gomi K (2008) DNA Res 15:173–183

    Article  CAS  Google Scholar 

  199. Christensen T, Woeldike H, Boel E et al (1988) Biotechnology 6:1419–1422

    Article  CAS  Google Scholar 

  200. Archer DB, Peberdy JF (1997) Crit Rev Biotechnol 17:273–306

    Article  CAS  Google Scholar 

  201. Novozymes (2008) Available at http://www.novozymes.com/en/MainStructure/Productfinder/. Accessed 20 Jan 2009

  202. NCBE. Available at http://www.ncbe.reading.ac.uk/ncbe/materials/enzymes/termamylliquid.html. Accessed 20 Jan 2009

  203. Goodfrey T, West S (1996) Industrial enzymology. Stockton, Macmillan, New York, London

    Google Scholar 

  204. DSM (2008) Available at http://www.dsm.com/en_US/html/dfs/news_items/preventase_approved_in_Singapore_and_NL.htm. Accessed 20 Jan 2009

  205. FDA (2006) The 2006 exposure assessment for acrylamide. Available at http://www.cfsan.fda.gov/∼dms/acryexpo/acryex5.htm. Accessed 20 Jan 2009

  206. Lopez M, Edens L (2005) J Agric Food Chem 53:7944–7949

    Article  CAS  Google Scholar 

  207. Edens L, Dekker P, Van der Hoeven R et al (2005) J Agric Food Chem 53:7950–7957

    Article  CAS  Google Scholar 

  208. AMFEP. Association of manufacturers and formulators of enzyme products. Available at http://www.amfep.org/list.html. Accessed 20 Jan 2009

  209. Alberts-Schonberg G, Alberts AW (1980) Hypocholesteremic fermentation products and process of preparation. US Patent 4,231,938

    Google Scholar 

  210. Tobert JA (2003) Nat Rev Drug Discov 2:517–526

    Article  CAS  Google Scholar 

  211. Punt PJ, van Biezen N, Conesa A et al (2002) Trends Biotechnol 20:200–211

    Article  CAS  Google Scholar 

  212. van den Hondel CAMJJ, Punt PJ, van Gorcom RFM (1991) Heterologous gene expression in fungi. In: Bennet JW, Lause LL (eds) More genetic manipulations of filamentous fungi. Academic, Orlando, FL

    Google Scholar 

  213. Guillemette T, van Peij N, Goosen T et al (2007) BMC Genomics 8:158

    Article  CAS  Google Scholar 

  214. Ward PP, Lo JY, Duke M et al (1992) Biotechnology 10:784–789

    Article  CAS  Google Scholar 

  215. Tamalampudi S, Talukder M, Hama S et al (2007) Appl Microbiol Biotechnol 75:387–395

    Article  CAS  Google Scholar 

  216. Larsen MW, Bornscheuer UT, Hult K (2008) Protein Expr Purif 62:90–97

    Article  CAS  Google Scholar 

  217. Stephanopoulos G, Alper H, Moxley J (2004) Nat Biotechnol 22:1261–1267

    Article  CAS  Google Scholar 

  218. Hermann T (2004) Curr Opin Biotechnol 15:444–448

    Article  CAS  Google Scholar 

  219. Duarte NC, Herrgard MJ, Palsson BO (2004) Genome Res 14:1298–1309

    Article  CAS  Google Scholar 

  220. Nookaew I, Jewett MC, Meechai A et al (2008) BMC Syst Biol 2:15

    Article  CAS  Google Scholar 

  221. Herrgard MJ, Swainston N, Dobson P et al (2008) Nat Biotechnol 26:1155–1160

    Article  CAS  Google Scholar 

  222. Burgard AP, Pharkya P, Maranas CD (2003) Biotechnol Bioeng 84:647–657

    Article  CAS  Google Scholar 

  223. Pharkya P, Burgard AP, Maranas CD (2004) Genome Res 14:2367–2376

    Article  CAS  Google Scholar 

  224. Patil KR, Rocha I, Forster J et al (2005) BMC Bioinformatics 6:308

    Article  CAS  Google Scholar 

  225. Patil KR, Nielsen J (2005) Proc Natl Acad Sci USA 102:2685–2689

    Article  CAS  Google Scholar 

  226. Grotkjaer T, Winther O, Regenberg B et al (2006) Bioinformatics 22:58–67

    Article  CAS  Google Scholar 

  227. Cakir T, Patil KR et al (2006) Integration of metabolome data with metabolic networks reveals reporter reactions. Molecular Systems Biology 2(50):1–11

    Google Scholar 

  228. Akesson M, Forster J, Nielsen J (2004) Metab Eng 6:285–293

    Article  CAS  Google Scholar 

  229. Cakir T, Efe C, Dikicioglu D et al (2007) Biotechnol Prog 23:320–326

    Article  CAS  Google Scholar 

  230. Otero JM, Panagiotou G, Olsson L (2007) Adv Biochem Eng Biotechnol 108:1–40

    CAS  Google Scholar 

  231. Nissen TL, Kielland-Brandt MC, Nielsen J et al (2000) Metab Eng 2:69–77

    Article  CAS  Google Scholar 

  232. Bro C, Regenberg B, Forster J et al (2006) Metab Eng 8:102–111

    Article  CAS  Google Scholar 

  233. Boyd DA, Cvitkovitch DG, Hamilton IR (1995) J Bacteriol 177:2622–2627

    CAS  Google Scholar 

  234. Dikicioglu D, Pir P, Onsan ZI et al (2008) Appl Environ Microbiol 74:5809–5816

    Article  CAS  Google Scholar 

  235. Hutter A, Oliver SG (1998) Appl Microbiol Biotechnol 49:511–516

    Article  CAS  Google Scholar 

  236. Andersen MR, Nielsen ML, Nielsen J (2008) Mol Syst Biol 4:13

    Article  CAS  Google Scholar 

  237. Vongsangnak W, Olsen P, Hansen K et al (2008) BMC Genomics 9:14

    Article  CAS  Google Scholar 

  238. Hutchinson CR, Kennedy J, Park C et al (2000) Antonie Van Leeuwenhoek 78:287–295

    Article  CAS  Google Scholar 

  239. Kennedy J, Auclair K, Kendrew SG et al (1999) Science 284:1368–1372

    Article  CAS  Google Scholar 

  240. Bailey C, Arst HN (1975) Eur J Biochem 51:573–577

    Article  CAS  Google Scholar 

  241. Hicks JK, Yu JH, Keller NP et al (1997) EMBO J 16:4916–4923

    Article  CAS  Google Scholar 

  242. Christensen BE, Kaasgaard S (2000) World Patent Application, WO 00/39322

    Google Scholar 

  243. Jacobs DI, Olsthoorn MMA, Maillet I et al (2009) Fungal Genet Biol 46:S141–S152

    Article  CAS  Google Scholar 

  244. Rabinovich E, Kerem A, Frohlich KU et al (2002) Mol Cell Biol 22:626–634

    Article  CAS  Google Scholar 

  245. Yan Q, Lennarz WJ (2002) J Biol Chem 6:47692–47700

    Article  Google Scholar 

  246. de Groot MJL, Daran-Lapujade P, van Breukelen B et al (2007) Microbiology 153:3864–3878

    Article  CAS  Google Scholar 

  247. Primrose S, Twyman R (2006) Principles of gene manipulation and genomics. Blackwell, Oxford

    Google Scholar 

  248. Bai FW, Anderson WA, Moo-Young M (2008) Biotechnol Adv 26:89–105

    Article  CAS  Google Scholar 

  249. Zanin GM, Santana CC, Bon EPS et al (2000) Appl Biochem Biotechnol 84–6:1147–1161

    Article  Google Scholar 

  250. Bulthuis BA, Gatenby AA, Haynie SL et al (2002) Method for the production of glycerol by recombinant organisms. E. I. du Ponte de Nemours and Company, Wilmington, DE

    Google Scholar 

  251. Geertman JM, van Maris AJ, van Dijken JP et al (2006) Metab Eng 8:532–542

    Article  CAS  Google Scholar 

  252. Zelle RM, de Hulster E, van Winden WA et al (2008) Appl Environ Microbiol 74:2766–2777

    Article  CAS  Google Scholar 

  253. Berovic M, Legisa M (2007) Biotechnol Annu Rev 13:303–343

    Article  CAS  Google Scholar 

  254. Forster A, Aurich A, Mauersberger S et al (2007) Appl Microbiol Biotechnol 75:1409–1417

    Article  CAS  Google Scholar 

  255. Huang YL, Mann K, Novak JM et al (1998) Biotechnol Prog 14:800–806

    Article  CAS  Google Scholar 

  256. Raspor P, Goranovic D (2008) Crit Rev Biotechnol 28:101–124

    Article  CAS  Google Scholar 

  257. Ishida N, Suzuki T, Tokuhiro K et al (2006) J Biosci Bioeng 101:172–177

    Article  CAS  Google Scholar 

  258. Chatterjee R, Millard CS, Champion K et al (2001) Appl Environ Microbiol 67:148–154

    Article  CAS  Google Scholar 

  259. Lee PC, Lee SY, Hong SH et al (2002) Appl Microbiol Biotechnol 58:663–668

    Article  CAS  Google Scholar 

  260. Lee PC, Schmidt-Dannert C (2002) Appl Microbiol Biotechnol 60:1–11

    Article  CAS  Google Scholar 

  261. Lee SJ, Lee DY, Kim TY et al (2005) Appl Environ Microbiol 71:7880–7887

    Article  CAS  Google Scholar 

  262. Liu YP, Zheng P, Sun ZH et al (2008) J Chem Technol Biotechnol 83:722–729

    Article  CAS  Google Scholar 

  263. Georgi T, Rittmann D, Wendisch VF (2005) Metab Eng 7:291–301

    Article  CAS  Google Scholar 

  264. Koffas MAG, Jung GY, Stephanopoulos G (2003) Metab Eng 5:32–41

    Article  CAS  Google Scholar 

  265. Ohnishi J, Mitsuhashi S, Hayashi M et al (2002) Appl Microbiol Biotechnol 58:217–223

    Article  CAS  Google Scholar 

  266. Yakandawala N, Romeo T, Friesen AD et al (2008) Appl Microbiol Biotechnol 78:283–291

    Article  CAS  Google Scholar 

  267. Berry A (1996) Trends Biotechnol 14:250–256

    Article  CAS  Google Scholar 

  268. Bongaerts JM, Kramer M, Muller U et al (2001) Metab Eng 3:289–300

    Article  CAS  Google Scholar 

  269. Lutke-Eversloh T, Stephanopoulos G (2007) Appl Microbiol Biotechnol 75:103–110

    Article  CAS  Google Scholar 

  270. Qi WW, Vannelli T, Breinig S et al (2007) Metab Eng 9:268–276

    Article  CAS  Google Scholar 

  271. Qi Y, Zhao RX, Cao HX et al (2002) J Cell Biochem 86:79–89

    Article  CAS  Google Scholar 

  272. Shimizu H, Tanaka H, Nakato A et al (2003) Bioprocess Biosyst Eng 25:291–298

    CAS  Google Scholar 

  273. Kimura E (2003) Adv Biochem Eng Biotechnol 79:37–57

    CAS  Google Scholar 

  274. Branduardi P, Fossati T, Sauer M et al (2007) PLoS One 2:e1092

    Article  CAS  Google Scholar 

  275. Manoj K (2002) Production of ascorbic acid. US Patent 6,358,715

    Google Scholar 

  276. Perkins JB, Sloma A, Hermann T et al (1999) J Ind Microbiol Biotechnol 22:8–18

    Article  CAS  Google Scholar 

  277. Stahmann KP, Revuelta JL, Seulberger H (2000) Appl Microbiol Biotechnol 53:509–516

    Article  CAS  Google Scholar 

  278. Zhu YB, Chen X, Chen T et al (2007) FEMS Microbiol Lett 266:224–230

    Article  CAS  Google Scholar 

  279. Robin J, Jakobsen M, Beyer M et al (2001) Appl Microbiol Biotechnol 57:357–362

    Article  CAS  Google Scholar 

  280. Chen Y, Deng W, Wu JQ et al (2008) Appl Environ Microbiol 74:1820–1828

    Article  CAS  Google Scholar 

  281. Banerjee UC, Saxena B, Chisti Y (1992) Biotechnol Adv 10:577–595

    Article  CAS  Google Scholar 

  282. Elander RP (2003) Appl Microbiol Biotechnol 61:385–392

    CAS  Google Scholar 

  283. Fjaervik E, Zotchev SB (2005) Appl Microbiol Biotechnol 67:436–443

    Article  CAS  Google Scholar 

  284. Yoon YJ, Kim ES, Hwang YS et al (2004) Appl Microbiol Biotechnol 63:626–634

    Article  CAS  Google Scholar 

  285. Pearson D, Ward OP (1988) J Appl Bacteriol 65:195–202

    Article  Google Scholar 

  286. Rowe GE, Margaritis A (2004) Biotechnol Bioeng 86:377–388

    Article  CAS  Google Scholar 

  287. Leonard E, Yan YJ, Koffas MAG (2006) Metab Eng 8:172–181

    Article  CAS  Google Scholar 

  288. Ralston L, Subramanian S, Matsuno M et al (2005) Plant Physiol 137:1375–1388

    Article  CAS  Google Scholar 

  289. Ro DK, Douglas CJ (2004) J Biol Chem 279:2600–2607

    Article  CAS  Google Scholar 

  290. Yan YJ, Chemler J, Huang LX et al (2005) Appl Environ Microbiol 71:3617–3623

    Article  CAS  Google Scholar 

  291. Becker JVW, Armstrong GO, Van der Merwe MJ et al (2003) FEMS Yeast Res 4:79–85

    Article  CAS  Google Scholar 

  292. Beekwilder J, Wolswinkel R, Jonker H et al (2006) Appl Environ Microbiol 72:5670–5672

    Article  CAS  Google Scholar 

  293. Zhang YS, Li SZ, Li J et al (2006) J Am Chem Soc 128:13030–13031

    Article  CAS  Google Scholar 

  294. Yamano Y, Yoshizawa M, Ito M (1999) J Nutr Sci Vitaminol 45:49–62

    Article  CAS  Google Scholar 

  295. Alper H, Miyaoku K, Stephanopoulos G (2005) Nat Biotechnol 23:612–616

    Article  CAS  Google Scholar 

  296. Yoon SH, Park HM, Kim JE et al (2007) Biotechnol Prog 23:599–605

    Article  CAS  Google Scholar 

  297. Wang CW, Oh MK, Liao JC (1999) Biotechnol Bioeng 62:235–241

    Article  CAS  Google Scholar 

  298. DeJong JM, Liu YL, Bollon AP et al (2006) Biotechnol Bioeng 93:212–224

    Article  CAS  Google Scholar 

  299. Engels B, Dahm P, Jennewein S (2008) Metab Eng 10:201–206

    Article  CAS  Google Scholar 

  300. Carter OA, Peters RJ, Croteau R (2003) Phytochemistry 64:425–433

    Article  CAS  Google Scholar 

  301. Asadollahi MA, Maury J, Møller K et al (2007) Biotechnol Bioeng 99:666–677

    Article  CAS  Google Scholar 

  302. Kealey JT, Liu L, Santi DV et al (1998) Proc Natl Acad Sci USA 95:505–509

    Article  CAS  Google Scholar 

  303. Wattanachaisaereekul S, Lantz AE, Nielsen ML et al (2008) Metab Eng 10:246–254

    Article  CAS  Google Scholar 

  304. Prathumpai W, Flitter SJ, McIntyre M et al (2004) Appl Microbiol Biotechnol 65:714–719

    Article  CAS  Google Scholar 

  305. Kusumoto KI, Matsushita-Morita M, Furukawa I et al (2008) J Appl Microbiol 105:1711–1719

    Article  CAS  Google Scholar 

  306. Chill L, Trinh L, Azadi P et al (2008) Biotechnol Bioeng 102:828–844

    Article  CAS  Google Scholar 

  307. Talabardon M, Yang ST (2005) Biotechnol Prog 21:1389–1400

    Article  CAS  Google Scholar 

  308. Carlsen M, Nielsen J (2001) Appl Microbiol Biotechnol 57:346–349

    CAS  Google Scholar 

  309. de Vries RP (2008) A genomic look at physiology and extracellular enzymes of Aspergillus in relation to utilization of plant matter. In: Varga J, Samson RA (eds) Aspergillus in the genomic era. Wageningen Academic, The Netherlands

    Google Scholar 

  310. Shankar SK, Mulimani VH (2007) Bioresour Technol 98:958–961

    Article  CAS  Google Scholar 

  311. Westers L, Westers H, Quax WJ (2004) Biochim Biophys Acta 1694:299–310

    Article  CAS  Google Scholar 

  312. Zukowski MM, Stabinsky Y, Levitt M (1990) Subtilisin analogs. US Patent 4,914,031

    Google Scholar 

  313. Pedersen H, Beyer M, Nielsen J (2000) Appl Microbiol Biotechnol 53:272–277

    Article  CAS  Google Scholar 

  314. DSM. DSM nutritional products. Available at http://www.dsm.com/en_US/html/dnp/prod_vit_b2.htm. Accessed 20 Jan 2009

  315. Cameron DC, Altaras NE, Hoffman ML et al (1998) Biotechnol Prog 14:116–125

    Article  CAS  Google Scholar 

  316. Nakamura CE, Whited GM (2003) Curr Opin Biotechnol 14:454–459

    Article  CAS  Google Scholar 

  317. Tong IT, Liao HH, Cameron DC (1991) Appl Environ Microbiol 57:3541–3546

    CAS  Google Scholar 

  318. Suriyamongkol P, Weselake R, Narine S et al (2007) Biotechnol Adv 25:148–175

    Article  CAS  Google Scholar 

  319. Suthers PF, Cameron DC (2001) Production of 3-hydroxypropionic acid in recombinant organisms. PCT WO 01-16346

    Google Scholar 

  320. Ensley BD, Ratzkin BJ, Osslund TD et al (1983) Science 222:167–169

    Article  CAS  Google Scholar 

  321. Weyler W, Dodge TC, Lauff JJ et al (1999) Microbial production of indigo. US Patent 5,866,396

    Google Scholar 

  322. Werner RG (2004) J Biotechnol 113:171–182

    Article  CAS  Google Scholar 

  323. Ro DK, Paradise EM, Ouellet M et al (2006) Nature 440:940–943

    Article  CAS  Google Scholar 

  324. Choi JH, Lee SJ, Lee SY (2003) Appl Environ Microbiol 69:4737–4742

    Article  CAS  Google Scholar 

  325. Chandran SS, Yi J, Draths KM et al (2003) Biotechnol Prog 19:808–814

    Article  CAS  Google Scholar 

  326. Blank LM, Kuepfer L, Sauer U (2005) Genome Biol 6:R49

    Article  CAS  Google Scholar 

  327. David H, Akesson M, Nielsen J (2003) Eur J Biochem 270:4243–4253

    Article  CAS  Google Scholar 

  328. Sun JB, Lu X et al (2007) Metabolic peculiarities of Aspergillus niger disclosed by comparative metabolic genomics. Genome Biol 8(9)

    Google Scholar 

  329. Kjeldsen T (2000) Appl Microbiol Biotechnol 54:277–286

    Article  CAS  Google Scholar 

  330. Markussen J, Fiil N, Hansen MT et al (1990) DNA-sequence encoding biosynthetic insulin precursors and process for preparing the insulin precursors and human insulin. US Patent 4,916,212

    Google Scholar 

  331. Joosten V, Christien L, van den Hondel C et al (2003) Microb Cell Fact 2:1

    Article  Google Scholar 

  332. Valenzuela P, Medina A, Rutter WJ (1982) Nature 298:347–350

    Article  CAS  Google Scholar 

  333. Kim MD, Rhee SK, Seo JH (2001) J Biotechnol 85:41–48

    Article  CAS  Google Scholar 

  334. Chemier JA, Fowler ZL, Koffas MA et al (2009) Adv Enzymol Relat Areas Mol Biol 76:151–217

    CAS  Google Scholar 

  335. van Maris AJA, Winkler AA, Kuyper M et al (2007) Adv Biochem Eng Biotechnol 108:179–204

    Google Scholar 

  336. Saitoh S, Ishida N, Onishi T et al (2005) Appl Environ Microbiol 71:2789–2792

    Article  CAS  Google Scholar 

  337. Maury J, Asadollahi MA, Moller K et al (2005) Adv Biochem Eng Biotechnol 100:19–51

    CAS  Google Scholar 

  338. Maury J, Asadollahi MA, Moller K et al (2008) FEBS Lett 582:4032–4038

    Article  CAS  Google Scholar 

  339. Carlson R, Srienc F (2006) J Biotechnol 124:561–573

    Article  CAS  Google Scholar 

  340. Zhang B, Carlson R, Srienc F (2006) Appl Environ Microbiol 72:536–543

    Article  CAS  Google Scholar 

  341. Steen EJ, Chan R, Prasad N et al (2008) Microb Cell Fact 7:36

    Article  CAS  Google Scholar 

  342. Sauer M, Branduardi P, Valli M et al (2004) Appl Environ Microbiol 70:6086–6091

    Article  CAS  Google Scholar 

  343. Bro C, Knudsen S, Regenberg B et al (2005) Appl Environ Microbiol 71:6465–6472

    Article  CAS  Google Scholar 

  344. Hirasawa T, Yoshikawa K, Nakakura Y et al (2007) J Biotechnol 131:34–44

    Article  CAS  Google Scholar 

  345. Pizarro F, Vargas FA, Agosin E (2007) Yeast 24:977–991

    Article  CAS  Google Scholar 

  346. Wattanachaisaereekul S (2007) Transcriptome data using reporter metabolites for 6-MSA production in recombinant strain. Technical University of Denmark, Kgs Lyngby, Denmark

    Google Scholar 

  347. Bro C, Regenberg B, Nielsen J (2003) Biotechnol Bioeng 85:269–276

    Article  CAS  Google Scholar 

  348. Pizarro FJ, Jewett MC, Nielsen J et al (2008) Appl Environ Microbiol 74:6358–6368

    Article  CAS  Google Scholar 

  349. Abbott DA, Suir E, van Maris AJA et al (2008) Appl Environ Microbiol 74:5759–5768

    Article  CAS  Google Scholar 

  350. Bundy JG, Papp B, Harmston R et al (2007) Genome Res 17:510–519

    Article  CAS  Google Scholar 

  351. Devantier R, Scheithauer B, Villas-Bôas SG et al (2005) Biotechnol Bioeng 90:703–714

    Article  CAS  Google Scholar 

  352. Villas-Bôas SG, Åkesson M, Nielsen J (2005) FEMS Yeast Res 5:703–709

    Article  CAS  Google Scholar 

  353. Salusjarvi L, Poutanen M, Pitkanen JP et al (2003) Yeast 20:295

    Article  CAS  Google Scholar 

  354. Cheng JS, Qiao B, Yuan YJ (2008) Appl Microbiol Biotechnol 81:327–338

    Article  CAS  Google Scholar 

  355. Zuzuarregui A, Monteoliva L, Gil C et al (2006) Appl Environ Microbiol 72:836–847

    Article  CAS  Google Scholar 

  356. Salusjarvi L, Kankainen M et al (2008) Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae. Microbial Cell Factories 7(18):1–16

    Google Scholar 

  357. Usaite R, Wohlschlegel J, Venable JD et al (2008) J Proteome Res 7:266–275

    Article  CAS  Google Scholar 

  358. Dos Santos MM, Thygesen G, Kötter P et al (2003) FEMS Yeast Res 4:59–68

    Article  CAS  Google Scholar 

  359. Kleijn RJ, Geertman JM, Nfor BK et al (2007) FEMS Yeast Res 7:216–231

    Article  CAS  Google Scholar 

  360. Snitkin ES, Dudley AM et al (2008) Model-driven analysis of experimentally determined growth phenotypes for 465 yeast gene deletion mutants under 16 different conditions. Genome Biol 9(9):RI 40

    Google Scholar 

  361. Grotkjaer T, Christakopoulos P, Nielsen J et al (2005) Metab Eng 7:437–444

    Article  CAS  Google Scholar 

  362. Raghevendran V, Gombert AK, Christensen B et al (2004) Yeast 21:769–779

    Article  CAS  Google Scholar 

  363. Carlson R, Fell D, Srienc F (2002) Biotechnol Bioeng 79:121–134

    Article  CAS  Google Scholar 

  364. Herrgard MJ, Lee BS, Portnoy V et al (2006) Genome Res 16:627–635

    Article  CAS  Google Scholar 

  365. Hjersted JL, Henson MA, Mahadevan R (2007) Biotechnol Bioeng 97:1190–1204

    Article  CAS  Google Scholar 

  366. Pocsi I, Miskei M et al (2005) Comparison of gene expression signatures of diamide, H2O2 and menadione exposed Aspergillus nidulans cultures - linking genome-wide transcriptional changes to cellular physiology. Bmc Genomics 6(182):1–18

    Google Scholar 

  367. Sims AH, Robson GD, Hoyle DC et al (2004) Fungal Genet Biol 41:199–212

    Article  CAS  Google Scholar 

  368. Malavazi I, Savoldi M, Di Mauro SMZ et al (2006) Eukaryot Cell 5:1688–1704

    Article  CAS  Google Scholar 

  369. Breakspear A, Momany M (2007) Eukaryot Cell 6:1697–1700

    Article  CAS  Google Scholar 

  370. Malavazi I, Savoldi M, da Silva Ferreira ME et al (2007) Mol Microbiol 66:74–99

    Article  CAS  Google Scholar 

  371. Bok J, Hoffmeister D, Maggio-Hall L et al (2006) Chem Biol 13:31–37

    Article  CAS  Google Scholar 

  372. Mogensen J, Nielsen H, Hofmann G et al (2006) Fungal Genet Biol 43:593–603

    Article  CAS  Google Scholar 

  373. Ray A, Macwana S, Ayoubi P et al (2004) BMC Genomics 5:22

    Article  Google Scholar 

  374. Sims AH, Gent ME, Lanthaler K et al (2005) Appl Environ Microbiol 71:2737–2747

    Article  CAS  Google Scholar 

  375. David H, Hofmann G, Oliveira A et al (2006) Genome Biol 7:R108

    Article  CAS  Google Scholar 

  376. David H, Ozcelik I, Hofmann G et al (2008) BMC Genomics 9:163

    Article  CAS  Google Scholar 

  377. Andersen MR, Vongsangnak W, Panagiotou G et al (2008) Proc Natl Acad Sci USA 105:4387–4392

    Article  CAS  Google Scholar 

  378. Jorgensen TR, Goosen T, van den Hondel CAMJJ et al (2009) BMC Genomics 10:44

    Article  CAS  Google Scholar 

  379. Andersen MR, Lehmann L, Nielsen J (2009) Systemic analysis of the response of Aspergillus niger to ambient pH. Genome Biology 10(5):R47

    Google Scholar 

  380. Salazar M, Vongsangnak W, Panagiotou G, Andersen MR, Nielsen J (2009) Uncovering transcriptional regulation of glycerol metabolism in Aspergilli through genome-wide gene expression data analysis. Mol Genet Genomics 282(6):571–586

    Google Scholar 

  381. Perrin R, Fedorova N, Bok J et al (2007) PLoS Pathog 3:e50

    Article  CAS  Google Scholar 

  382. Maeda H, Sano M, Maruyama Y et al (2004) Appl Microbiol Biotechnol 65:74–83

    Article  CAS  Google Scholar 

  383. Masai K, Maruyama J, Sakamoto K et al (2006) Appl Microbiol Biotechnol 71:881–891

    Article  CAS  Google Scholar 

  384. Kimura S, Maruyama J, Takeuchi M et al (2008) Biosci Biotechnol Biochem 72:499–505

    Article  CAS  Google Scholar 

  385. Tamano K, Sano M, Yamane N et al (2008) Fungal Genet Biol 45:139–151

    Article  CAS  Google Scholar 

  386. Chang P, Wilkinson J, Horn B et al (2007) Appl Microbiol Biotechnol 77:917–925

    Article  CAS  Google Scholar 

  387. Price M, Yu J, Nierman W et al (2006) FEMS Microbiol Lett 255:275–279

    Article  CAS  Google Scholar 

  388. Kim J, Yu J, Mahoney N et al (2008) Int J Food Microbiol 122:49–60

    Article  CAS  Google Scholar 

  389. O’Brian G, Fakhoury A, Payne G (2003) Fungal Genet Biol 39:118–127

    Article  CAS  Google Scholar 

  390. Price M, Conners S, Tachdjian S et al (2005) Fungal Genet Biol 42:506–518

    Article  CAS  Google Scholar 

  391. Andersen MR, Nielsen J (2009) Fungal Genet Biol 46:S180–S190

    Article  CAS  Google Scholar 

  392. Edwards JS, Palsson BO (2000) Proc Natl Acad Sci USA 97:5528–5533

    Article  CAS  Google Scholar 

  393. Reed JL, Vo TD, Schilling CH et al (2003) Genome Biol 4

    Google Scholar 

  394. Feist AM, Henry CS, Reed JL et al (2007) Mol Syst Biol 3:121

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Chemical and Biological Engineering – Systems Biology, Chalmers University of Technology, Kemigården 4, Göteborg, 41296, Sweden

    Marta Papini, Margarita Salazar & Jens Nielsen

Authors
  1. Marta Papini
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  2. Margarita Salazar
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  3. Jens Nielsen
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Correspondence to Jens Nielsen .

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Editors and Affiliations

  1. Inst. Bioverfahrenstechnik, TU Braunschweig, Gaußstraße 17, Braunschweig, 38106, Germany

    Christoph Wittmann

  2. Inst. Bioverfahrenstechnik, TU Braunschweig, Gaußstraße 17, Braunschweig, 38106, Germany

    Rainer Krull

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Papini, M., Salazar, M., Nielsen, J. (2010). Systems Biology of Industrial Microorganisms. In: Wittmann, C., Krull, R. (eds) Biosystems Engineering I. Advances in Biochemical Engineering / Biotechnology, vol 120. Springer, Berlin, Heidelberg. https://doi.org/10.1007/10_2009_59

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