De novo metabolic engineering and the promise of synthetic DNA

Advances in Biochemical Engineering/Biotechnology

Volumn 120, Issue , 2010, Pages 101-131

  Klein Marcuschamer, Daniel ^a   Yadav, Vikramaditya G ^a   Ghaderi, Adel ^a   Stephanopoulos, Gregory N ^a  

^a Massachusetts Institute of Technology Cambridge   (United States)

Author keywords

Gene circuits; Metabolic control; Oligonucleotide synthesis; Regulatory engineering; Synthetic biology

Indexed keywords

DNA;

ARTICLE; BIOGENESIS; CHEMISTRY; GENE LIBRARY; GENETICS; METABOLIC ENGINEERING; METHODOLOGY;

BIOGENESIS; DNA; GENE LIBRARY; METABOLIC ENGINEERING;

EID: 79954988442     PISSN: 07246145     EISSN: None     Source Type: Book Series    
DOI: 10.1007/10_2009_52     Document Type: Article

References (105)

1. Raab RM, Tyo K, Stephanopoulos G (2005) Metabolic engineering. Adv Biochem Eng Biotechnol 100:1-17
2. Stephanopoulos G (1999) Metabolic fluxes and metabolic engineering. Metab Eng 1:1-11
3. Hamilton SR, Bobrowicz P, Bobrowicz B, Davidson RC, Li H, Mitchell T, Nett JH, Rausch S, Stadheim TA, Wischnewski H, Wildt S, Gerngross TU (2003) Production of complex human glycoproteins in yeast. Science 301:1244-1246
4. Gerngross TU (2004) Advances in the production of human therapeutic proteins in yeast and filamentous fungi. Nat Biotechnol 22:1409-1414
5. Betengaugh M, Bentley W (2008) Metabolic engineering in the 21st century: meeting global challenges of sustainability and health. Curr Opin Biotechnol 19:411-413
6. Shendure J, Mitra RD, Varma C, Church GM (2004) Advanced sequencing technologies: methods and goals. Nat Rev Genet 5:335-344
7. Tian J, Gong H, Sheng N, Zhou X, Gulari E, Gao X, Church GM (2004) Accurate multiplex gene synthesis from programmable DNA microchips. Nature 432:1050-1054
8. Dwyer MA, Looger LL, Hellinga HW (2004) Computational design of a biologically active enzyme. Science 304:1967-1971
9. Park JH, Lee SY, Kim TY, Kim HU (2008) Application of systems biology for bioprocess development. Trends Biotechnol 26:404-412
10. Benner SA, Sismour M (2005) Synthetic biology. Nat Rev Genet 6:533-543
11. Sprinzak D, Elowitz MB (2005) Reconstruction of genetic circuits. Nature 438:443-448
12. Brown DM (1993) A brief history of oligonucleotide synthesis. In: Methods in molecular biology, vol 20. Humana, Totowa, NJ, pp 1-17
13. Itakura K, Rossi JJ, Wallace RB (1984) Synthesis and uses of synthetic oligonucleotides. Annu Rev Biochem 53:323-356
14. Ahmad S, Kamal MZ, Sankaranarayanan R, Rao NM (2008) Thermostable Bacillus subtilis lipases: in vitro evolution and structural insight. J Mol Biol 381:324-340
15. Alkan C, Karakoc E, Nadeau J, Sahinalp S, Zhang K (2006) RNA-RNA interaction prediction and antisense RNA target search. J Comput Biol 13:267-282
16. Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA 3rd, Smith HO (2008) Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319:1215-1220
17. Santos CN, Stephanopoulos G (2008) Combinatorial engineering of microbes for optimizing cellular phenotype. Curr Opin Chem Biol 12:168-176
18. Alper H (2006) Development of systematic and combinatorial approaches for the metabolic engineering of microorganisms. Ph.D. thesis, Massachusetts Institute of Technology, Cambridge, MA
19. Keasling JD (2008) Synthetic biology for synthetic chemistry. ACS Chem Biol 3:64-76
20. Smolke CD, Keasling JD (2002) Effect of gene location, mRNA secondary structures, and RNase sites on expression of two genes in an engineered operon. Biotechnol Bioeng 80:762-776
21. Gebauer F, Hentze M (2004) Molecular mechanisms of translational control. Nat Rev Mol Cell Biol 5:827-835
22. Grunberg-Manago M (1999) Messenger RNA stability and its role in control of gene expression in bacteria and phages. Annu Rev Genet 33:193-227
23. Kozak M (2005) Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene 361:13-37
24. Tijsterman M, Ketting R, Plasterk R (2002) The genetics of RNA silencing. Annu Rev Genet 36:489-519
25. Wray GA, Babbitt CC (2008) Enhancing gene regulation. Science 321:1300-1301
26. Hammer K, Mijakovic I, Jensen PR (2006) Synthetic promoter libraries: tuning of gene expression. Trends Biotechnol 24:53-55
27. Alper H, Fischer C, Nevoigt E, Stephanopoulos G (2005) Tuning genetic control through promoter engineering. Proc Natl Acad Sci 102:12678-12683
28. Pfleger BF, Pitera DJ, Smolke CD, Keasling JD (2006) Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat Biotechnol 24:1027-1032
29. Munroe SH, Zhu J (2006) Overlapping transcripts, double-stranded RNA and antisense regulation: a genomic perspective. Cell Mol Life Sci 63:2102-2118
30. Brink MF, Verbeet MP, de Boer HA (1995) Specialized ribosomes: highly specific translation in vivo of a single targetted mRNA species. Gene 156:215-222
31. Hui A, de Boer HA (1987) Specialized ribosome system: preferential translation of a single mRNA species by a subpopulation of mutated ribosomes in Escherichia coli. Proc Natl Acad Sci USA 84:4762-4766
32. Fargo D, Zhang M, Gillham N, Boynton J (1998) Shine-Dalgrano-like sequences are not required for translation of chloroplast mRNAs in Chlamydomonas reinhardtii chloroplasts or in Escherichia coli. Mol Gen Genet 257:271-282
33. Zuker M, Matthews D, Turner D (1999) Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In: Barciszewski J, Clark B (eds) RNA biochemistry and biotechnology: proceedings of the NATO advanced research workshop, Poznan, Poland, 10-17 October 1998. Springer, Berlin, pp 11-43
34. Hofacker IL (2003) Vienna RNA secondary structure server. Nucleic Acids Res 31:3429-3431
35. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406-3415
36. Both G, Furuichi Y, Muthukrishnan S, Shatkin A (1975) Ribosome binding to reovirus mRNA in protein synthesis requires 50 terminal 7-methylguanosine. Cell 6:185-195
37. Kozak M (1986) Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44:283-292
38. Shabalina S, Ogurtsov A, Rogozin I, Koonin E, Lipman D (2004) Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals. Nucleic Acids Res 32:1774-1782
39. Winkler W, Nahvi A, Roth A, Collins J, Breaker R (2004) Control of gene expression by a natural metabolite-responsive ribozyme. Nature 428:281-286
40. Kane JF (1995) Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli. Curr Opin Biotechnol 6:494-500
41. Burgess-Brown NA, Sharma S, Sobott F, Loenarz C, Oppermann U, Gileadi O (2008) Codon optimization can improve expression of human genes in Escherichia coli: a multi-gene study. Protein Expr Purif 59:94-102
42. Kleber-Janke T, Becker WM (2000) Use of modified BL21(DE3) Escherichia coli cells for high-level expression of recombinant peanut allergens affected by poor codon usage. Protein Expr Purif 19:419-424
43. Seidel HM, Pompliano DL, Knowles JR (1992) Phosphonate biosynthesis-molecularcloning of the gene for phosphoenolpyruvate mutase from Tetrahymena pyriformis and overexpression of the gene-product in Escherichia coli. Biochemistry 31:2598-2608
44. Fuglsang A (2003) Codon optimizer: a freeware tool for codon optimization. Protein Expr Purif 31:247-249
45. Cai YJ, Sun J, Wang J, Ding YR, Tian N, Liao XR, Xu WB (2008) Optimizing the codon usage of synthetic gene with QPSO algorithm. J Theor Biol 254:123-127
46. Hebert C, Valdes J, Bentley W (2008) Beyond silencing-engineering applications of RNA interference and antisense technology for altering cellular phenotype. Curr Opin Biotechnol 19:500-505
47. Tomari Y, Zamore P (2005) Perspective: machines for RNAi. Genes Dev 19:517-529
48. Khvorova A, Reynolds A, Jayasena S (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell 115:209-216
49. Schwarz D, Hutvágner G, Haley B, Zamore P (2002) Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways. Mol Cell 10:537-548
50. Desai RP, Papoutsakis ET (1999) Antisense RNA strategies for metabolic engineering of Clostridium acetobutylicum. Appl Environ Microbiol 65:936-945
51. Nakayama S, Kosaka T, Hirakawa H, Matsuura K, Yoshino S, Furukawa K (2008) Metabolic engineering for solvent productivity by downregulation of the hydrogenase gene cluster hupCBA in Clostridium saccharoperbutylacetonicum strain N1-4. Appl Microbiol Biotechnol 78:483-493
52. Majors B, Betenbaugh M, Chiang G (2007) Links between metabolism and apoptosis in mammalian cells: applications for anti-apoptosis engineering. Metab Eng 9:317-326
53. Friedman S, Shah S (2006) Control of gene expression via light activated RNA interference. US Patent Application 11/148,89154. Gredell J, Berger A, Walton S (2008) Impact of target mRNA structure on siRNA silencing efficiency: a large-scale study. Biotechnol Bioeng 100:744-755
54. Gredell J, Berger A, Walton S (2008) Impact of target mRNA structure on siRNA silencing efficiency: a large-scale study. Biotechnol Bioeng 100:744-755
55. Yiu S, Wong P, Lam T, Mui Y, Kung H, Lin M, Cheung Y (2005) Filtering of ineffective siRNAs and improved siRNA design tool. Bioinformatics 21:144-151
56. Widner B, Behr R, Von Dollen S, Tang M, Heu T, Sloma A, Sternberg D, DeAngelis PL, Weigel PH, Brown S (2005) Hyaluronic acid production in Bacillus subtilis. Appl Environ Microbiol 71:3747-3752
57. Yu H, Stephanopoulos G (2008) Metabolic engineering of Escherichia coli for biosynthesis of hyaluronic acid. Metab Eng 10:24-32
58. Chien LJ, Lee CK (2007) Hyaluronic acid production by recombinant Lactococcus lactis. Appl Microbiol Biotechnol 77:339-346
59. Gordon E, Horsefield R, Swarts HGP, de Pont J, Neutze R, Snijder A (2008) Effective highthroughput overproduction of membrane proteins in Escherichia coli. Protein Expr Purif 62:1-8
60. Simon EM, Nanney DL, Doerder FP (2008) The "Tetrahymena pyriformis" complex of cryptic species. Biodivers Conserv 17:365-380
61. Kannan N, Taylor SS, Zhai YF, Venter JC, Manning G (2007) Structural and functional diversity of the microbial kinome. PLoS Biol 5:467-478
62. Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu DY, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcon LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC (2007) The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS Biol 5:398-431
63. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu DY, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66-74
64. Yooseph S, Sutton G, Rusch DB, Halpern AL, Williamson SJ, Remington K, Eisen JA, Heidelberg KB, Manning G, Li WZ, Jaroszewski L, Cieplak P, Miller CS, Li HY, Mashiyama ST, Joachimiak MP, van Belle C, Chandonia JM, Soergel DA, Zhai YF, Natarajan K, Lee S, Raphael BJ, Bafna V, Friedman R, Brenner SE, Godzik A, Eisenberg D, Dixon JE, Taylor SS, Strausberg RL, Frazier M, Venter JC (2007) The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol 5:432-466
65. Lorenz P, Liebton K, Niehaus F, Eck J (2002) Screening for novel enzymes for biocatalytic processes: accessing the metagenome as a resource of novel functional sequence space. Curr Opin Biotechnol 13:572-577
66. Lorenz P, Eck J (2005) Metagenomics and industrial applications. Nat Rev Microbiol 3:510-516
67. Asara JM, Schweitzer MH, Freimark LM, Phillips M, Cantley LC (2007) Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry. Science 316:280-285
68. Jensen PR, Hammer K (1998) Artificial promoters for metabolic optimization. Biotechnol Bioeng 58:191-195
69. Jensen PR, Hammer K (1998) The sequence of spacers between the consensus sequences modulates the strength of prokaryotic promoters. Appl Environ Microbiol 64:82-87
70. Miksch G, Bettenworth F, Friehs K, Flaschel E, Saalbach A, Twellmann T, Nattkemper TW (2005) Libraries of synthetic stationary-phase and stress promoters as a tool for fine-tuning of expression of recombinant proteins in Escherichia coli. J Biotechnol 120:25-37
71. Goler JA, Bramlett BW, Peccoud J (2008) Genetic design: rising above the sequence. Trends Biotechnol 26:538-544
72. Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403:339-342
73. Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403:335-338
74. Guet CC, Elowitz MB, Hsing WH, Leibler S (2002) Combinatorial synthesis of genetic networks. Science 296:1466-1470
75. Cai Y, Hartnett B, Gustafsson C, Peccoud J (2007) A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics 23:2760-2767
76. Miyazaki K, Arnold FH (1999) Exploring nonnatural evolutionary pathways by saturation mutagenesis: rapid improvement of protein function. J Mol Evol 49:716-720
77. Voigt CA, Mayo SL, Arnold FH, Wang ZG (2001) Computational method to reduce the search space for directed protein evolution. Proc Natl Acad Sci USA 98:3778-3783
78. Van den Brulle J, Fischer M, Langmann T, Horn G, Waldmann T, Arnold S, Fuhrmann M, Schatz O, O'Connell T, O'Connell D, Auckenthaler A, Schwer H (2008) A novel solid phase technology for high-throughput gene synthesis. Biotechniques 45:340-343
79. Stemmer WP (1994) Rapid evolution of a protein in vitro by DNA shuffling. Nature 370:389-391
80. Ostermeier M (2003) Synthetic gene libraries: in search of the optimal diversity. Trends Biotechnol 21:244-247
81. Coco WM, Encell LP, Levinson WE, Crist MJ, Loomis AK, Licato LL, Arensdorf JJ, Sica N, Pienkos PT, Monticello DJ (2002) Growth factor engineering by degenerate homoduplex gene family recombination. Nat Biotechnol 20:1246-1250
82. Ness JE, Kim S, Gottman A, Pak R, Krebber A, Borchert TV, Govindarajan S, Mundorff EC, Minshull J (2002) Synthetic shuffling expands functional protein diversity by allowing amino acids to recombine independently. Nat Biotechnol 20:1251-1255
83. el Hawrani AS, Sessions RB, Moreton KM, Holbrook JJ (1996) Guided evolution of enzymes with new substrate specificities. J Mol Biol 264:97-110
84. Munir KM, French DC, Loeb LA (1993) Thymidine kinase mutants obtained by random sequence selection. Proc Natl Acad Sci USA 90:4012-4016
85. Lunzer M, Miller SP, Felsheim R, Dean AM (2005) The biochemical architecture of an ancient adaptive landscape. Science 310:499-501
86. Yoshikuni Y, Ferrin TE, Keasling JD (2006) Designed divergent evolution of enzyme function. Nature 440:1078-1082
87. Yoshikuni Y, Martin VJ, Ferrin TE, Keasling JD (2006) Engineering cotton (+)-deltacadinene synthase to an altered function: germacrene D-4-ol synthase. Chem Biol 13:91-98
88. Ohnuma S, Narita K, Nakazawa T, Ishida C, Takeuchi Y, Ohto C, Nishino T (1996) A role of the amino acid residue located on the fifth position before the first aspartate-rich motif of farnesyl diphosphate synthase on determination of the final product. J Biol Chem 271:30748-30754
89. Solem C, Jensen PR (2002) Modulation of gene expression made easy. Appl Environ Microbiol 68:2397-2403
90. Arnould S, Chames P, Perez C, Lacroix E, Duclert A, Epinat JC, Stricher F, Petit AS, Patin A, Guillier S, Rolland S, Prieto J, Blanco FJ, Bravo J, Montoya G, Serrano L, Duchateau P, Paques F (2006) Engineering of large numbers of highly specific homing endonucleases that induce recombination on novel DNA targets. J Mol Biol 355:443-458
91. Smith J, Grizot S, Arnould S, Duclert A, Epinat JC, Chames P, Prieto J, Redondo P, Blanco FJ, Bravo J, Montoya G, Paques F, Duchateau P (2006) A combinatorial approach to create artificial homing endonucleases cleaving chosen sequences. Nucleic Acids Res 34:e149
92. Hurt JA, Thibodeau SA, Hirsh AS, Pabo CO, Joung JK (2003) Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection. Proc Natl Acad Sci USA 100:12271-12276
93. Beerli RR, Barbas CF 3rd (2002) Engineering polydactyl zinc-finger transcription factors. Nat Biotechnol 20:135-141
94. Porteus MH, Carroll D (2005) Gene targeting using zinc finger nucleases. Nat Biotechnol 23:967-973
95. Park KS, Jang YS, Lee H, Kim JS (2005) Phenotypic alteration and target gene identification using combinatorial libraries of zinc finger proteins in prokaryotic cells. J Bacteriol 187:5496-5499
96. Park KS, Lee DK, Lee H, Lee Y, Jang YS, Kim YH, Yang HY, Lee SI, Seol W, Kim JS (2003) Phenotypic alteration of eukaryotic cells using randomized libraries of artificial transcription factors. Nat Biotechnol 21:1208-1214
97. Fischer CR, Klein-Marcuschamer D, Stephanopoulos G (2008) Selection and optimization of microbial hosts for biofuels production. Metab Eng 10:295-304
98. Klein-Marcuschamer D, Stephanopoulos G (2008) Assessing the potential of mutational strategies to elicit new phenotypes in industrial strains. Proc Natl Acad Sci USA 105:2319-2324
99. Smith HO, Hutchison CA 3rd, Pfannkoch C, Venter JC (2003) Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci USA 100:15440-15445
100. Forster AC, Church GM (2007) Synthetic biology projects in vitro. Genome Res 17:1-6
101. Noireaux V, Bar-Ziv R, Godefroy J, Salman H, Libchaber A (2005) Toward an artificial cell based on gene expression in vesicles. Phys Biol 2:P1-P8
102. Forster AC, Church GM (2006) Towards synthesis of a minimal cell. Mol Syst Biol 2:45
103. Lartigue C, Glass JI, Alperovich N, Pieper R, Parmar PP, Hutchison CA 3rd, Smith HO, Venter JC (2007) Genome transplantation in bacteria: changing one species to another. Science 317:632-638
104. Yin E, Le YL, Pei JJ, Shao WL, Yang QY (2008) High-level expression of the xylanase from Thermomyces lanuginosus in Escherichia coli. World J Microbiol Biotechnol 24:275-280
105. Puigbo P, Guzman E, Romeu A, Garcia-Vallve S (2007) OPTIMIZER: a web server for optimizing the codon usage of DNA sequences. Nucleic Acids Res 35:W126-W131