Streamlining the Design-to-Build Transition with Build-Optimization Software Tools

ACS Synthetic Biology

Volumn 6, Issue 3, 2017, Pages 485-496

  Oberortner, Ernst ^a,b   Cheng, Jan Fang ^a,b   Hillson, Nathan J ^a,b,c   Deutsch, Samuel ^a,b  

^a DOE JOINT GENOME INSTITUTE   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c JOINT BIOENERGY INSTITUTE   (United States)

Author keywords

bioCAD CAM; design build test; DNA synthesis; synthetic biology

Indexed keywords

SYNTHETIC DNA; DNA;

ARTICLE; CODON USAGE; COMPUTER AIDED DESIGN; DNA INTEGRATION; DNA SEQUENCE; DNA SYNTHESIS; HUMAN; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROMOTER REGION; SOFTWARE; SYNTHETIC BIOLOGY; DNA REPLICATION; GENETIC ENGINEERING; GENETICS; PROCEDURES;

COMPUTER-AIDED DESIGN; DNA; DNA REPLICATION; GENES, SYNTHETIC; GENETIC ENGINEERING; SOFTWARE; SYNTHETIC BIOLOGY;

EID: 85018519480     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.6b00200     Document Type: Article

References (39)

1. Koppel, N. and Balskus, E. P. ( 2016 ) Exploring and Understanding the Biochemical Diversity of the Human Microbiota Cell Chem. Biol. 23, 18-30 10.1016/j.chembiol.2015.12.008
2. Walker, M. C. and Chang, M. C. ( 2014 ) Natural and engineered biosynthesis of fluorinated natural products Chem. Soc. Rev. 43, 6527-6536 10.1039/C4CS00027G
3. Rinke, C., Schwientek, P., Sczyrba, A., Ivanova, N. N., Anderson, I. J., Cheng, J. F., Darling, A., Malfatti, S., Swan, B. K., Gies, E. A., Dodsworth, J. A., Hedlund, B. P., Tsiamis, G., Sievert, S. M., Liu, W. T., Eisen, J. A., Hallam, S. J., Kyrpides, N. C., Stepanauskas, R., Rubin, E. M., Hugenholtz, P., and Woyke, T. ( 2013 ) Insights into the phylogeny and coding potential of microbial dark matter Nature 499, 431-437 10.1038/nature12352
4. Long, P. E., Williams, K. H., Hubbard, S. S., and Banfield, J. F. ( 2016 ) Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes Trends Microbiol. 24 ( 8 ) 600-610 10.1016/j.tim.2016.04.006
5. Paddon, C. J., Westfall, P. J., Pitera, D. J., Benjamin, K., Fisher, K., McPhee, D., Leavell, M. D., Tai, A., Main, A., Eng, D., Polichuk, D. R., Teoh, K. H., Reed, D. W., Treynor, T., Lenihan, J., Fleck, M., Bajad, S., Dang, G., Dengrove, D., Diola, D., Dorin, G., Ellens, K. W., Fickes, S., Galazzo, J., Gaucher, S. P., Geistlinger, T., Henry, R., Hepp, M., Horning, T., Iqbal, T., Jiang, H., Kizer, L., Lieu, B., Melis, D., Moss, N., Regentin, R., Secrest, S., Tsuruta, H., Vazquez, R., Westblade, L. F., Xu, L., Yu, M., Zhang, Y., Zhao, L., Lievense, J., Covello, P. S., Keasling, J. D., Reiling, K. K., Renninger, N. S., and Newman, J. D. ( 2013 ) High-level semi-synthetic production of the potent antimalarial artemisinin Nature 496, 528-532 10.1038/nature12051
6. Burgard, A., Burk, M. J., Osterhout, R., Van Dien, S., and Yim, H. ( 2016 ) Development of a commercial scale process for production of 1,4-butanediol from sugar Curr. Opin. Biotechnol. 42, 118-125 10.1016/j.copbio.2016.04.016
7. Cheong, S., Clomburg, J. M., and Gonzalez, R. ( 2016 ) Energy-and carbon-efficient synthesis of functionalized small molecules in bacteria using non-decarboxylative Claisen condensation reactions Nat. Biotechnol. 34, 556-561 10.1038/nbt.3505
8. Ham, T. S., Dmytriv, Z., Plahar, H., Chen, J., Hillson, N. J., and Keasling, J. D. ( 2012 ) Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools Nucleic Acids Res. 40, e141 10.1093/nar/gks531
9. Markowitz, V. M., Chen, I. M., Palaniappan, K., Chu, K., Szeto, E., Grechkin, Y., Ratner, A., Jacob, B., Huang, J., Williams, P., Huntemann, M., Anderson, I., Mavromatis, K., Ivanova, N. N., and Kyrpides, N. C. ( 2012 ) IMG: the Integrated Microbial Genomes database and comparative analysis system Nucleic Acids Res. 40, D115-122 10.1093/nar/gkr1044
10. Kanehisa, M. and Goto, S. ( 2000 ) KEGG: kyoto encyclopedia of genes and genomes Nucleic Acids Res. 28, 27-30 10.1093/nar/28.1.27
11. Geer, L. Y., Marchler-Bauer, A., Geer, R. C., Han, L., He, J., He, S., Liu, C., Shi, W., and Bryant, S. H. ( 2010 ) The NCBI BioSystems database Nucleic Acids Res. 38, D492-496 10.1093/nar/gkp858
12. Madsen, C., McLaughlin, J. A., Misirli, G., Pocock, M., Flanagan, K., Hallinan, J., and Wipat, A. ( 2016 ) The SBOL Stack: A Platform for Storing, Publishing, and Sharing Synthetic Biology Designs ACS Synth. Biol. 5, 487-497 10.1021/acssynbio.5b00210
13. Nielsen, A. A., Der, B. S., Shin, J., Vaidyanathan, P., Paralanov, V., Strychalski, E. A., Ross, D., Densmore, D., and Voigt, C. A. ( 2016 ) Genetic circuit design automation Science 352, aac7341 10.1126/science.aac7341
14. Chen, J., Densmore, D., Ham, T. S., Keasling, J. D., and Hillson, N. J. ( 2012 ) DeviceEditor visual biological CAD canvas J. Biol. Eng. 6, 1 10.1186/PREACCEPT-1967068768635731
15. Czar, M. J., Cai, Y., and Peccoud, J. ( 2009 ) Writing DNA with GenoCAD Nucleic Acids Res. 37, W40-47 10.1093/nar/gkp361
16. Bilitchenko, L., Liu, A., Cheung, S., Weeding, E., Xia, B., Leguia, M., Anderson, J. C., and Densmore, D. ( 2011 ) Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems PLoS One 6, e18882 10.1371/journal.pone.0018882
17. Roehner, N., Young, E. M., Voigt, C. A., Gordon, D. B., and Densmore, D. ( 2016 ) Double Dutch: A Tool for Designing Combinatorial Libraries of Biological Systems ACS Synth. Biol. 5, 507-517 10.1021/acssynbio.5b00232
18. Richardson, S. M., Wheelan, S. J., Yarrington, R. M., and Boeke, J. D. ( 2006 ) GeneDesign: rapid, automated design of multikilobase synthetic genes Genome Res. 16, 550-556 10.1101/gr.4431306
19. Espah Borujeni, A., Channarasappa, A. S., and Salis, H. M. ( 2014 ) Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites Nucleic Acids Res. 42, 2646-2659 10.1093/nar/gkt1139
20. Na, D. and Lee, D. ( 2010 ) RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression Bioinformatics 26, 2633-2634 10.1093/bioinformatics/btq458
21. Reeve, B., Hargest, T., Gilbert, C., and Ellis, T. ( 2014 ) Predicting translation initiation rates for designing synthetic biology Front. Bioeng. Biotechnol. 2, 1 10.3389/fbioe.2014.00001
22. Salis, H. M., Mirsky, E. A., and Voigt, C. A. ( 2009 ) Automated design of synthetic ribosome binding sites to control protein expression Nat. Biotechnol. 27, 946-950 10.1038/nbt.1568
23. Hillson, N. J., Rosengarten, R. D., and Keasling, J. D. ( 2012 ) j5 DNA assembly design automation software ACS Synth. Biol. 1, 14-21 10.1021/sb2000116
24. Appleton, E., Tao, J., Haddock, T., and Densmore, D. ( 2014 ) Interactive assembly algorithms for molecular cloning Nat. Methods 11, 657-662 10.1038/nmeth.2939
25. Linshiz, G., Stawski, N., Goyal, G., Bi, C., Poust, S., Sharma, M., Mutalik, V., Keasling, J. D., and Hillson, N. J. ( 2014 ) PR-PR: cross-platform laboratory automation system ACS Synth. Biol. 3, 515-524 10.1021/sb4001728
26. Galdzicki, M., Clancy, K. P., Oberortner, E., Pocock, M., Quinn, J. Y., Rodriguez, C. A., Roehner, N., Wilson, M. L., Adam, L., Anderson, J. C., Bartley, B. A., Beal, J., Chandran, D., Chen, J., Densmore, D., Endy, D., Grunberg, R., Hallinan, J., Hillson, N. J., Johnson, J. D., Kuchinsky, A., Lux, M., Misirli, G., Peccoud, J., Plahar, H. A., Sirin, E., Stan, G. B., Villalobos, A., Wipat, A., Gennari, J. H., Myers, C. J., and Sauro, H. M. ( 2014 ) The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology Nat. Biotechnol. 32, 545-550 10.1038/nbt.2891
27. Roehner, N., Beal, J., Clancy, K., Bartley, B., Misirli, G., Grunberg, R., Oberortner, E., Pocock, M., Bissell, M., Madsen, C., Nguyen, T., Zhang, M., Zhang, Z., Zundel, Z., Densmore, D., Gennari, J. H., Wipat, A., Sauro, H. M., and Myers, C. J. ( 2016 ) Sharing Structure and Function in Biological Design with SBOL 2.0 ACS Synth. Biol. 5, 498-506 10.1021/acssynbio.5b00215
28. 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. Q., Segall-Shapiro, T. H., Calvey, C. H., Parmar, P. P., Hutchison, C. A., 3rd, Smith, H. O., and Venter, J. C. ( 2010 ) Creation of a bacterial cell controlled by a chemically synthesized genome Science 329, 52-56 10.1126/science.1190719
29. Annaluru, N., Muller, H., Mitchell, L. A., Ramalingam, S., Stracquadanio, G., Richardson, S. M., Dymond, J. S., Kuang, Z., Scheifele, L. Z., Cooper, E. M., Cai, Y., Zeller, K., Agmon, N., Han, J. S., Hadjithomas, M., Tullman, J., Caravelli, K., Cirelli, K., Guo, Z., London, V., Yeluru, A., Murugan, S., Kandavelou, K., Agier, N., Fischer, G., Yang, K., Martin, J. A., Bilgel, M., Bohutski, P., Boulier, K. M., Capaldo, B. J., Chang, J., Charoen, K., Choi, W. J., Deng, P., DiCarlo, J. E., Doong, J., Dunn, J., Feinberg, J. I., Fernandez, C., Floria, C. E., Gladowski, D., Hadidi, P., Ishizuka, I., Jabbari, J., Lau, C. Y., Lee, P. A., Li, S., Lin, D., Linder, M. E., Ling, J., Liu, J., Liu, J., London, M., Ma, H., Mao, J., McDade, J. E., McMillan, A., Moore, A. M., Oh, W. C., Ouyang, Y., Patel, R., Paul, M., Paulsen, L. C., Qiu, J., Rhee, A., Rubashkin, M. G., Soh, I. Y., Sotuyo, N. E., Srinivas, V., Suarez, A., Wong, A., Wong, R., Xie, W. R., Xu, Y., Yu, A. T., Koszul, R., Bader, J. S., Boeke, J. D., and Chandrasegaran, S. ( 2014 ) Total synthesis of a functional designer eukaryotic chromosome Science 344, 55-58 10.1126/science.1249252
30. Hutchison, C. A., 3rd, Chuang, R. Y., Noskov, V. N., Assad-Garcia, N., Deerinck, T. J., Ellisman, M. H., Gill, J., Kannan, K., Karas, B. J., Ma, L., Pelletier, J. F., Qi, Z. Q., Richter, R. A., Strychalski, E. A., Sun, L., Suzuki, Y., Tsvetanova, B., Wise, K. S., Smith, H. O., Glass, J. I., Merryman, C., Gibson, D. G., and Venter, J. C. ( 2016 ) Design and synthesis of a minimal bacterial genome Science 351, aad6253 10.1126/science.aad6253
31. Kosuri, S. and Church, G. M. ( 2014 ) Large-scale de novo DNA synthesis: technologies and applications Nat. Methods 11, 499-507 10.1038/nmeth.2918
32. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., and Sayers, E. W. ( 2009 ) GenBank Nucleic Acids Res. 37, D26-31 10.1093/nar/gkn723
33. Hentrich, C. and Zdun, U. ( 2006 ) Patterns for business object model integration in process-driven and service-oriented architectures, In Proceedings of the 2006 conference on Pattern languages of programs, pp 1-14, ACM, Portland, Oregon, USA.
34. Villalobos, A., Ness, J. E., Gustafsson, C., Minshull, J., and Govindarajan, S. ( 2006 ) Gene Designer: a synthetic biology tool for constructing artificial DNA segments BMC Bioinf. 7, 285 10.1186/1471-2105-7-285
35. Christen, M., Deutsch, S., and Christen, B. ( 2015 ) Genome Calligrapher: A Web Tool for Refactoring Bacterial Genome Sequences for de Novo DNA Synthesis ACS Synth. Biol. 4, 927-934 10.1021/acssynbio.5b00087
36. Holland, R. C., Down, T. A., Pocock, M., Prlic, A., Huen, D., James, K., Foisy, S., Drager, A., Yates, A., Heuer, M., and Schreiber, M. J. ( 2008 ) BioJava: an open-source framework for bioinformatics Bioinformatics 24, 2096-2097 10.1093/bioinformatics/btn397
37. Zhang, Z., Nguyen, T., Roehner, N., Misirli, G., Pocock, M., Oberortner, E., Samineni, M., Zundel, Z., Beal, J., Clancy, K., Wipat, A., and Myers, C. J. ( 2015 ) libSBOLj 2.0: A Java Library to Support SBOL 2.0 IEEE Life Sciences Letters 1, 34-37 10.1109/LLS.2016.2546546
38. Sharp, P. M., Tuohy, T. M., and Mosurski, K. R. ( 1986 ) Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes Nucleic Acids Res. 14, 5125-5143 10.1093/nar/14.13.5125
39. Gibson, D. G. ( 2011 ) Enzymatic assembly of overlapping DNA fragments Methods Enzymol. 498, 349-361 10.1016/B978-0-12-385120-8.00015-2