Biology by design: From top to bottom and back

Journal of Biomedicine and Biotechnology

Volumn 2010, Issue , 2010, Pages

  Leonard, Joshua N ^a,b   Fritz, Brian R ^a,b   Timmerman, Laura E ^a   Daringer, Nichole M ^a,c   Jewett, Michael C ^a,b,c  

^a Northwestern University   (United States)

^b NORTHWESTERN UNIVERSITY   (United States)

^c NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOPOLYMER;

BIOCHEMISTRY; BIOENGINEERING; BIOLOGY; BIOTRANSFORMATION; CONCEPTUAL FRAMEWORK; DEVICE; REVIEW; STUDY DESIGN; SYNTHETIC BIOLOGY; ANIMAL; BIOTECHNOLOGY; GENETIC ENGINEERING; HUMAN; METHODOLOGY;

ANIMALS; BIOTECHNOLOGY; GENETIC ENGINEERING; HUMANS; SYNTHETIC BIOLOGY;

EID: 78650735548     PISSN: 11107243     EISSN: 11107251     Source Type: Journal    
DOI: 10.1155/2010/232016     Document Type: Review

References (97)

1. Costanzo M., Baryshnikova A., Bellay J., Kim Y., Spear E. D., Sevier C. S., Ding H., Koh J. L.Y., Toufighi K., Mostafavi S., Prinz J., St. Onge R. P., Vandersluis B., Makhnevych T., Vizeacoumar F. J., Alizadeh S., Bahr S., Brost R. L., Chen Y., Cokol M., Deshpande R., Li Z., Lin Z. -Y., Liang W., Marback M., Paw J., Luis B. -J.S., Shuteriqi E., Tong A. H.Y., van Dyk N., Wallace I. M., Whitney J. A., Weirauch M. T., Zhong G., Zhu H., Houry W. A., Brudno M., Ragibizadeh S., Papp B., Pl C., Roth F. P., Giaever G., Nislow C., Troyanskaya O. G., Bussey H., Bader G. D., Gingras A. -C., Morris Q. D., Kim P. M., Kaiser C. A., Myers C. L., Andrews B. J., Boone C., The genetic landscape of a cell Science 2010 327 5964 425 431
2. Gell M., van Noort V., Yus E., Chen W.-H., Leigh-Bell J., Michalodimitrakis K., Yamada T., Arumugam M., Doerks T., Khner S., Rode M., Suyama M., Schmidt S., Gavin A.-C., Bork P., Serrano L., Transcriptome complexity in a genome-reduced bacterium Science 2009 326 5957 1268 1271
3. Khalil A. S., Collins J. J., Synthetic biology: applications come of age Nature Reviews Genetics 2010 11 5 367 379
4. Benner S. A., Sismour A. M., Synthetic biology Nature Reviews Genetics 2005 6 7 533 543
5. Baker D., Church G., Collins J., Endy D., Jacobson J., Keasling J., Modrich P., Smolke C., Weiss R., Engineering life: building a FAB for biology Scientific American 2006 294 6 44 51
6. Endy D., Foundations for engineering biology Nature 2005 438 7067 449 453
7. Purnick P. E. M., Weiss R., The second wave of synthetic biology: from modules to systems Nature Reviews Molecular Cell Biology 2009 10 6 410 422
8. Isaacs F. J., Dwyer D. J., Collins J. J., RNA synthetic biology Nature Biotechnology 2006 24 5 545 554
9. Carothers J. M., Goler J. A., Keasling J. D., Chemical synthesis using synthetic biology Current Opinion in Biotechnology 2009 20 4 498 503
10. Kwok R., Five hard truths for synthetic biology Nature 2010 463 7279 288 290
11. Bailey J. E., Toward a science of metabolic engineering Science 1991 252 5013 1668 1675
12. Nielsen J., Metabolic engineering Applied Microbiology and Biotechnology 2001 55 3 263 283
13. Atsumi S., Hanai T., Liao J. C., Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels Nature 2008 451 7174 86 89
14. Ro D.-K., Paradise E. M., Quellet M., Fisher K. J., Newman K. L., Ndungu J. M., Ho K. A., Eachus R. A., Ham T. S., Kirby J., Chang M. C. Y., Withers S. T., Shiba Y., Sarpong R., Keasling J. D., Production of the antimalarial drug precursor artemisinic acid in engineered yeast Nature 2006 440 7086 940 943
15. Steen E. J., Kang Y., Bokinsky G., Hu Z., Schirmer A., McClure A., Del Cardayre S. B., Keasling J. D., Microbial production of fatty-acid-derived fuels and chemicals from plant biomass Nature 2010 463 7280 559 562
16. Atsumi S., Wu T.-Y., Eckl E.-M., Hawkins S. D., Buelter T., Liao J. C., Engineering the isobutanol biosynthetic pathway in Escherichia coli by comparison of three aldehyde reductase/alcohol dehydrogenase genes Applied Microbiology and Biotechnology 2010 85 3 651 657
17. Zhang K., Sawaya M. R., Eisenberg D. S., Liao J. C., Expanding metabolism for biosynthesis of nonnatural alcohols Proceedings of the National Academy of Sciences of the United States of America 2008 105 52 20653 20658
18. Lewis J. C., Bastian S., Bennett C. S., Fu Y., Mitsuda Y., Chen M. M., Greenberg W. A., Wong C.-H., Arnold F. H., Chemoenzymatic elaboration of monosaccharides using engineered cytochrome P450BM3 demethylases Proceedings of the National Academy of Sciences of the United States of America 2009 106 39 16550 16555
19. Siegel J. B., Zanghellini A., Lovick H. M., Kiss G., Lambert A. R., St.Clair J. L., Gallaher J. L., Hilvert D., Gelb M. H., Stoddard B. L., Houk K. N., Michael F. E., Baker D., Computational design of an enzyme catalyst for a stereoselective bimolecular diels-alder reaction Science 2010 329 5989 309 313
20. Nielsen D. R., Leonard E., Yoon S.-H., Tseng H.-C., Yuan C., Prather K. L. J., Engineering alternative butanol production platforms in heterologous bacteria Metabolic Engineering 2009 11 4-5 262 273
21. Maury J., Asadollahi M. A., Mller K., Schalk M., Clark A., Formenti L. R., Nielsen J., Reconstruction of a bacterial isoprenoid biosynthetic pathway in Saccharomyces cerevisiae FEBS Letters 2008 582 29 4032 4038
22. Moon T. S., Yoon S.-H., Lanza A. M., Roy-Mayhew J. D., Prather K. L. J., Production of glucaric acid from a synthetic pathway in recombinant Escherichia coli Applied and Environmental Microbiology 2009 75 3 589 595
23. Hawkins K. M., Smolke C. D., Production of benzylisoquinoline alkaloids in Saccharomyces cerevisiae Nature Chemical Biology 2008 4 9 564 573
24. Dueber J. E., Wu G. C., Malmirchegini G. R., Moon T. S., Petzold C. J., Ullal A. V., Prather K. L. J., Keasling J. D., Synthetic protein scaffolds provide modular control over metabolic flux Nature Biotechnology 2009 27 8 753 759
25. Miles E. W., Rhee S., Davies D. R., The molecular basis of substrate channeling Journal of Biological Chemistry 1999 274 18 12193 12196
26. Spivey H. O., Ovdi J., Substrate channeling Methods 1999 19 2 306 321
27. Anderson J. C., Voigt C. A., Arkin A. P., Environmental signal integration by a modular and gate Molecular Systems Biology 2007 3, article 133
28. Gardner T. S., Cantor C. R., Collins J. J., Construction of a genetic toggle switch in Escherichia coli Nature 2000 403 6767 339 342
29. Tigges M., Marquez-Lago T. T., Stelling J., Fussenegger M., A tunable synthetic mammalian oscillator Nature 2009 457 7227 309 312
30. Salis H. M., Mirsky E. A., Voigt C. A., Automated design of synthetic ribosome binding sites to control protein expression Nature Biotechnology 2009 27 10 946 950
31. Sommer M. O. A., Church G. M., Dantas G., A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion Molecular Systems Biology 2010 6, article 360
32. Bayer T. S., Widmaier D. M., Temme K., Mirsky E. A., Santi D. V., Voigt C. A., Synthesis of methyl halides from biomass using engineered microbes Journal of the American Chemical Society 2009 131 18 6508 6515
33. Lynch M. D., Warnecke T., Gill R. T., SCALEs: multiscale analysis of library enrichment Nature Methods 2007 4 1 87 93
34. Bonomo J., Lynch M. D., Warnecke T., Price J. V., Gill R. T., Genome-scale analysis of anti-metabolite directed strain engineering Metabolic Engineering 2008 10 2 109 120
35. Wang H. H., Isaacs F. J., Carr P. A., Sun Z. Z., Xu G., Forest C. R., Church G. M., Programming cells by multiplex genome engineering and accelerated evolution Nature 2009 460 7257 894 898
36. Alper H., Moxley J., Nevoigt E., Fink G. R., Stephanopoulos G., Engineering yeast transcription machinery for improved ethanol tolerance and production Science 2006 314 5805 1565 1568
37. Alper H., Stephanopoulos G., Global transcription machinery engineering: a new approach for improving cellular phenotype Metabolic Engineering 2007 9 3 258 267
38. Gibson D. G., Glass J. I., Lartigue C., Noskov V. N., Chuang R. -Y., Algire M. A., Benders G. A., Montague M. G., Ma L., Moodie M. M., Merryman C., Vashee S., Krishnakumar R., Assad-Garcia N., Andrews-Pfannkoch C., Denisova E. A., Young L., Qi Z. -N., Segall-Shapiro T. H., Calvey C. H., Parmar P. P., Hutchison III C. A., Smith H. O., Venter J. C., Creation of a bacterial cell controlled by a chemically synthesized genome Science 2010 329 5987 52 56
39. Howard P. L., Chia M. C., Del Rizzo S., Liu F.-F., Pawson T., Redirecting tyrosine kinase signaling to an apoptotic caspase pathway through chimeric adaptor proteins Proceedings of the National Academy of Sciences of the United States of America 2003 100 20 11267 11272
40. Dueber J. E., Yeh B. J., Chak K., Lim W. A., Reprogramming control of an allosteric signaling switch through modular recombination Science 2003 301 5641 1904 1908
41. Dueber J. E., Yeh B. J., Bhattacharyya R. P., Lim W. A., Rewiring cell signaling: the logic and plasticity of eukaryotic protein circuitry Current Opinion in Structural Biology 2004 14 6 690 699
42. Bashor C. J., Helman N. C., Yan S., Lim W. A., Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics Science 2008 319 5869 1539 1543
43. Marcu-Malina V., van Dorp S., Kuball J., Re-targeting T-cells against cancer by gene-transfer of tumor-reactive receptors Expert Opinion on Biological Therapy 2009 9 5 579 591
44. Milone M. C., Fish J. D., Carpenito C., Carroll R. G., Binder G. K., Teachey D., Samanta M., Lakhal M., Gloss B., Danet-Desnoyers G., Campana D., Riley J. L., Grupp S. A., June C. H., Chimeric receptors containing CD137 signal transduction domains mediate enhanced survival of T cells and increased antileukemic efficacy in vivo Molecular Therapy 2009 17 8 1453 1464
45. Xu Y., Darcy P. K., Kershaw M. H., Tumor-specific dendritic cells generated by genetic redirection of Toll-like receptor signaling against the tumor-associated antigen, erbB2 Cancer Gene Therapy 2007 14 9 773 780
46. Conklin B. R., Hsiao E. C., Claeysen S., Dumuis A., Srinivasan S., Forsayeth J. R., Guettier J.-M., Chang W. C., Pei Y., McCarthy K. D., Nissenson R. A., Wess J., Bockaert J., Roth B. L., Engineering GPCR signaling pathways with RASSLs Nature Methods 2008 5 8 673 678
47. Chen Y. Y., Jensen M. C., Smolke C. D., Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems Proceedings of the National Academy of Sciences of the United States of America 2010 107 19 8531 8536
48. Rinaudo K., Bleris L., Maddamsetti R., Subramanian S., Weiss R., Benenson Y., A universal RNAi-based logic evaluator that operates in mammalian cells Nature Biotechnology 2007 25 7 795 801
49. Anderson J. C., Clarke E. J., Arkin A. P., Voigt C. A., Environmentally controlled invasion of cancer cells by engineered bacteria Journal of Molecular Biology 2006 355 4 619 627
50. Steidler L., Neirynck S., Huyghebaert N., Snoeck V., Vermeire A., Goddeeris B., Cox E., Remon J. P., Remaut E., Biological containment of genetically modified Lactococcus lactis for intestinal delivery of human interleukin 10 Nature Biotechnology 2003 21 7 785 789
51. Braat H., Rottiers P., Hommes D. W., Huyghebaert N., Remaut E., Remon J., van Deventer S. J. H., Neirynck S., Peppelenbosch M. P., Steidler L., A phase I trial with transgenic bacteria expressing interleukin-10 in Crohn's disease Clinical Gastroenterology and Hepatology 2006 4 6 754 759
52. Chen M.-T., Weiss R., Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana Nature Biotechnology 2005 23 12 1551 1555
53. Brenner K., Karig D. K., Weiss R., Arnold F. H., Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium Proceedings of the National Academy of Sciences of the United States of America 2007 104 44 17300 17304
54. Basu S., Gerchman Y., Collins C. H., Arnold F. H., Weiss R., A synthetic multicellular system for programmed pattern formation Nature 2005 434 7037 1130 1134
55. Danino T., Mondragn-Palomino O., Tsimring L., Hasty J., A synchronized quorum of genetic clocks Nature 2010 463 7279 326 330
56. Weber W., Daoud-El Baba M., Fussenegger M., Synthetic ecosystems based on airborne inter- and intrakingdom communication Proceedings of the National Academy of Sciences of the United States of America 2007 104 25 10435 10440
57. Weber W., Schoenmakers R., Keller B., Gitzinger M., Grau T., Baba M. D.-E., Sander P., Fussenegger M., A synthetic mammalian gene circuit reveals antituberculosis compounds Proceedings of the National Academy of Sciences of the United States of America 2008 105 29 9994 9998
58. van der Meer J. R., Belkin S., Where microbiology meets microengineering: design and applications of reporter bacteria Nature Reviews Microbiology 2010 8 7 511 522
59. Nielsen P. E., PNA technology Molecular Biotechnology 2004 26 3 233 248
60. Brudno Y., Liu D. R., Recent progress toward the templated synthesis and directed evolution of sequence-defined synthetic polymers Chemistry Biology 2009 16 3 265 276
61. Loakes D., Holliger P., Polymerase engineering: towards the encoded synthesis of unnatural biopolymers Chemical Communications 2009 31 4619 4631
62. Herdewijn P., Marlire P., Toward safe genetically modified organisms through the chemical diversification of nucleic acids Chemistry Biodiversity 2009 6 6 791 808
63. Benner S. A., Understanding nucleic acids using synthetic chemistry Accounts of Chemical Research 2004 37 10 784 797
64. Freier S. M., Altmann K.-H., The ups and downs of nucleic acid duplex stability: structure-stability studies on chemically-modified DNA:RNA duplexes Nucleic Acids Research 1997 25 22 4429 4443
65. Geyer C. R., Battersby T. R., Benner S. A., Nucleobase pairing in expanded Watson-Crick-like genetic information systems Structure 2003 11 12 1485 1498
66. Kaur H., Babu B. R., Maiti S., Perspectives on chemistry and therapeutic applications of locked nucleic acid (LNA) Chemical Reviews 2007 107 11 4672 4697
67. Ichida J. K., Zou K., Horhota A., Yu B., McLaughlin L. W., Szostak J. W., An in vitro selection system for TNA Journal of the American Chemical Society 2005 127 9 2802 2803
68. Wu T., Orgel L. E., Disulfide-linked oligonucleotide phosphorothioates: novel analogues of nucleic acids Journal of Molecular Evolution 1991 32 4 274 277
69. Summerton J., Weller D., Morpholino antisense oligomers: design, preparation, and properties Antisense and Nucleic Acid Drug Development 1997 7 3 187 195
70. Chaput J. C., Szostak J. W., TNA synthesis by DNA polymerases Journal of the American Chemical Society 2003 125 31 9274 9275
71. Fa M., Radeghieri A., Henry A. A., Romesberg F. E., Expanding the substrate repertoire of a DNA polymerase by directed evolution Journal of the American Chemical Society 2004 126 6 1748 1754
72. Sismour A. M., Lutz S., Park J.-H., Lutz M. J., Boyer P. L., Hughes S. H., Benner S. A., PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from human immunodeficiency virus-1 Nucleic Acids Research 2004 32 2 728 735
73. Wang L., Schultz P. G., Expanding the genetic code Angewandte Chemie International Edition 2005 44 1 34 66
74. Hecht S. M., Alford B. L., Kuroda Y., Kitano S., Chemical aminoacylation of tRNA's Journal of Biological Chemistry 1978 253 13 4517 4520
75. Murakami H., Ohta A., Ashigai H., Suga H., A highly flexible tRNA acylation method for non-natural polypeptide synthesis Nature Methods 2006 3 5 357 359
76. Wang L., Brock A., Herberich B., Schultz P. G., Expanding the genetic code of Escherichia coli Science 2001 292 5516 498 500
77. Kawakami T., Murakami H., Suga H., Messenger RNA-programmed incorporation of multiple N-methyl-amino acids into linear and cyclic peptides Chemistry Biology 2008 15 1 32 42
78. Fahnestock S., Rich A., Ribosome-catalyzed polyester formation Science 1971 173 994 340 343
79. Ohta A., Murakami H., Higashimura E., Suga H., Synthesis of polyester by means of genetic code reprogramming Chemistry Biology 2007 14 12 1315 1322
80. Ohta A., Yamagishi Y., Suga H., Synthesis of biopolymers using genetic code reprogramming Current Opinion in Chemical Biology 2008 12 2 159 167
81. Ledoux S., Uhlenbeck O. C., Different aa-tRNAs are selected uniformly on the ribosome Molecular Cell 2008 31 1 114 123
82. Doi Y., Ohtsuki T., Shimizu Y., Ueda T., Sisido M., Elongation factor Tu mutants expand amino acid tolerance of protein biosynthesis system Journal of the American Chemical Society 2007 129 46 14458 14462
83. Dedkova L. M., Fahmi N. E., Golovine S. Y., Hecht S. M., Enhanced D-amino acid incorporation into protein by modified ribosomes Journal of the American Chemical Society 2003 125 22 6616 6617
84. Chirkova A., Erlacher M., Micura R., Polacek N., Chemically engineered ribosomes: a new frontier in synthetic biology Current Organic Chemistry 2010 14 2 148 161
85. Hui A., de Boer H. A., Specialized ribosome system: preferential translation of a single mRNA species by a subpopulation of mutated ribosomes in Escherichia coli Proceedings of the National Academy of Sciences of the United States of America 1987 84 14 4762 4766
86. Rackham O., Chin J. W., Cellular logic with orthogonal ribosomes Journal of the American Chemical Society 2005 127 50 17584 17585
87. Wang K., Neumann H., Peak-Chew S. Y., Chin J. W., Evolved orthogonal ribosomes enhance the efficiency of synthetic genetic code expansion Nature Biotechnology 2007 25 7 770 777
88. Neumann H., Wang K., Davis L., Garcia-Alai M., Chin J. W., Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome Nature 2010 464 7287 441 444
89. Forster A. C., Church G. M., Towards synthesis of a minimal cell Molecular Systems Biology 2006 2, article 45
90. Forster A. C., Church G. M., Synthetic biology projects in vitro Genome Research 2007 17 1 1 6
91. Hold C., Panke S., Towards the engineering of in vitro systems Journal of the Royal Society Interface 2009 6 Suppl 4 S507 S521
92. Jewett M. C., Forster A. C., Update on designing and building minimal cells Current Opinion in Biotechnology 2010 21 5 697 703
93. Jewett M. C., Calhoun K. A., Voloshin A., Wuu J. J., Swartz J. R., An integrated cell-free metabolic platform for protein production and synthetic biology Molecular Systems Biology 2008 4, article 220
94. Jewett M. C., Swartz J. R., Mimicking the Escherichia coli cytoplasmic environment activates long-lived and efficient cell-free protein synthesis Biotechnology and Bioengineering 2004 86 1 19 26
95. Barrett O. P. T., Chin J. W., Evolved orthogonal ribosome purification for in vitro characterization Nucleic Acids Research 2010 38 8 2682 2691
96. Goerke A. R., Swartz J. R., High-level cell-free synthesis yields of proteins containing site-specific non-natural amino acids Biotechnology and Bioengineering 2009 102 2 400 416
97. Bujara M., Schmperli M., Billerbeck S., Heinemann M., Panke S., Exploiting cell-free systems: implementation and debugging of a system of biotransformations Biotechnology and Bioengineering 2010 106 3 376 389