Putting Synthesis into Biology: A Viral View of Genetic Engineering through De Novo Gene and Genome Synthesis

Chemistry and Biology

Volumn 16, Issue 3, 2009, Pages 337-347

  Mueller, Steffen ^a   Coleman, J Robert ^a   Wimmer, Eckard ^a  

^a STONY BROOK UNIVERSITY   (United States)

Author keywords

DNA; SYSBIO

Indexed keywords

DNA;

GENETIC ENGINEERING; GENETICS; GENOME; HUMAN; PROTEIN ENGINEERING; REVIEW; SYNTHESIS; VIRUS GENOME;

DNA; GENETIC ENGINEERING; GENOME; GENOME, VIRAL; HUMANS; PROTEIN ENGINEERING;

RNA VIRUSES;

EID: 62649117859     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2009.03.002     Document Type: Review

References (48)

1. Agarwal K.L., Buchi H., Caruthers M.H., Gupta N., Khorana H.G., Kleppe K., Kumar A., Ohtsuka E., Rajbhandary U.L., Van de Sande J.H., et al. Total synthesis of the gene for an alanine transfer ribonucleic acid from yeast. Nature 227 (1970) 27-34
2. Barany F. Genetic disease detection and DNA amplification using cloned thermostable ligase. Proc. Natl. Acad. Sci. USA 88 (1991) 189-193
3. Becker M.M., Graham R.L., Donaldson E.F., Rockx B., Sims A.C., Sheahan T., Pickles R.J., Corti D., Johnston R.E., Baric R.S., and Denison M.R. Synthetic recombinant bat SARS-like coronavirus is infectious in cultured cells and in mice. Proc. Natl. Acad. Sci. USA 105 (2008) 19944-19949
4. Blight K.J., Kolykhalov A.A., and Rice C.M. Efficient initiation of HCV RNA replication in cell culture. Science 290 (2000) 1972-1974
5. Carr, P.A., and Isaacs, F. (2006). rE.coli: whole genome engineering. Presented at the Second International Conference on Synthetic Biology (Synthetic Biology 2.0), May 20-22, Berkeley, CA.
6. Carr P.A., Park J.S., Lee Y.J., Yu T., Zhang S., and Jacobson J.M. Protein-mediated error correction for de novo DNA synthesis. Nucleic Acids Res. 32 (2004) e162
7. Caruthers M.H., Barone A.D., Beaucage S.L., Dodds D.R., Fisher E.F., McBride L.J., Matteucci M., Stabinsky Z., and Tang J.Y. Chemical synthesis of deoxyoligonucleotides by the phosphoramidite method. Methods Enzymol. 154 (1987) 287-313
8. Cello J., Paul A.V., and Wimmer E. Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science 297 (2002) 1016-1018
9. Chan L.Y., Kosuri S., and Endy D. Refactoring bacteriophage T7. Mol. Syst. Biol. 1 (2005) 2005.0018
10. Coleman J.R., Papamichail D., Skiena S., Futcher B., Wimmer E., and Mueller S. Virus attenuation by genome-scale changes in codon pair bias. Science 320 (2008) 1784-1787
11. Cowell M., and Bobe J. Straight talk with...Mac Cowell and Jason Bobe. Interview by Prashant Nair. Nat. Med. 15 (2009) 230-231
12. Czar M.J., Anderson J.C., Bader J.S., and Peccoud J. Gene synthesis demystified. Trends Biotechnol. 27 (2009) 63-72
13. Dewannieux M., Harper F., Richaud A., Letzelter C., Ribet D., Pierron G., and Heidmann T. Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements. Genome Res. 16 (2006) 1548-1556
14. Dymond J.S., Scheifele L.Z., Richardson S., Lee P., Chandrasegaran S., Bader J.S., and Boeke J.D. Teaching synthetic biology, bioinformatics and engineering to undergraduates: the interdisciplinary Build-a-Genome course. Genetics 181 (2009) 13-21
15. The Economist. (2006). Life 2.0. The Economist, September 2, 2006, pp. 67-70.
16. Edge M.D., Green A.R., Heathcliffe G.R., Meacock P.A., Schuch W., Scanlon D.B., Atkinson T.C., Newton C.R., and Markham A.F. Total synthesis of a human leukocyte interferon gene. Nature 292 (1981) 756-762
17. Ferretti L., Karnik S.S., Khorana H.G., Nassal M., and Oprian D.D. Total synthesis of a gene for bovine rhodopsin. Proc. Natl. Acad. Sci. USA 83 (1986) 599-603
18. Fodor S.P., Read J.L., Pirrung M.C., Stryer L., Lu A.T., and Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science 251 (1991) 767-773
19. Gibson D.G., Benders G.A., Andrews-Pfannkoch C., Denisova E.A., Baden-Tillson H., Zaveri J., Stockwell T.B., Brownley A., Thomas D.W., Algire M.A., et al. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319 (2008) 1215-1220
20. Goler J.A., Bramlett B.W., and Peccoud J. Genetic design: rising above the sequence. Trends Biotechnol. 26 (2008) 538-544
21. Goodman C. Engineering ingenuity at iGEM. Nat. Chem. Biol. 4 (2008) 13
22. Gupta N.K., Ohtsuka E., Sgaramella V., Buchi H., Kumar A., Weber H., and Khorana H.G. Studies on polynucleotides, 88. Enzymatic joining of chemically synthesized segments corresponding to the gene for alanine-tRNA. Proc. Natl. Acad. Sci. USA 60 (1968) 1338-1344
23. Gustafsson C., Govindarajan S., and Minshull J. Codon bias and heterologous protein expression. Trends Biotechnol. 22 (2004) 346-353
24. Herper M. Venter takes step toward synthetic cells. June 28, 2007. Available at:. Forbes (2007). http://www.forbes.com/2007/06/28/venter-synthetic-bacteria-tech-science-cx_mh_0628venter.html
25. Itakura K., Hirose T., Crea R., Riggs A.D., Heyneker H.L., Bolivar F., and Boyer H.W. Expression in Escherichia coli of a chemically synthesized gene for the hormone somatostatin. Science 198 (1977) 1056-1063
26. Kalman M., Cserpan I., Bajszar G., Dobi A., Horvath E., Pazman C., and Simoncsits A. Synthesis of a gene for human serum albumin and its expression in Saccharomyces cerevisiae. Nucleic Acids Res. 18 (1990) 6075-6081
27. Khorana H.G. Total synthesis of a gene. Science 203 (1979) 614-625
28. Kitamura N., Adler C., Martinko J., Nathenson S., and Wimmer E. The genome-linked protein of picornaviruses Vll. Genetic mapping of poliovirus VPg by protein and RNA sequence studies. Cell 21 (1980) 295-302
29. Kodumal S.J., Patel K.G., Reid R., Menzella H.G., Welch M., and Santi D.V. Total synthesis of long DNA sequences: synthesis of a contiguous 32-kb polyketide synthase gene cluster. Proc. Natl. Acad. Sci. USA 101 (2004) 15573-15578
30. Lartigue C., Glass J.I., Alperovich N., Pieper R., Parmar P.P., Hutchison III C.A., Smith H.O., and Venter J.C. Genome transplantation in bacteria: changing one species to another. Science 317 (2007) 632-638
31. Lee Y.N., and Bieniasz P.D. Reconstitution of an infectious human endogenous retrovirus. PLoS Pathog. 3 (2007) e10
32. Letsinger R.L., and Mahadevan V. Oligonucleotide synthesis on a polymer support. J. Am. Chem. Soc. 87 (1965) 3526-3527
33. Mueller S., Papamichail D., Coleman J.R., Skiena S., and Wimmer E. Reduction of the rate of poliovirus protein synthesis through large-scale codon deoptimization causes attenuation of viral virulence by lowering specific infectivity. J. Virol. 80 (2006) 9687-9696
34. Nirenberg M., and Leder P. RNA codewords and protein synthesis. The effect of trinucleotides upon the binding of srna to ribosomes. Science 145 (1964) 1399-1407
35. Pan W., Ravot E., Tolle R., Frank R., Mosbach R., Turbachova I., and Bujard H. Vaccine candidate MSP-1 from Plasmodium falciparum: a redesigned 4917 bp polynucleotide enables synthesis and isolation of full-length protein from Escherichia coli and mammalian cells. Nucleic Acids Res. 27 (1999) 1094-1103
36. Perry R.T., and Halsey N.A. The clinical significance of measles: a review. J. Infect. Dis. 189 Suppl 1 (2004) S4-S16
37. Picksley S.M., Parsons C.A., Kemper B., and West S.C. Cleavage specificity of bacteriophage T4 endonuclease VII and bacteriophage T7 endonuclease I on synthetic branch migratable Holliday junctions. J. Mol. Biol. 212 (1990) 723-735
38. Singh-Gasson S., Green R.D., Yue Y., Nelson C., Blattner F., Sussman M.R., and Cerrina F. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nat. Biotechnol. 17 (1999) 974-978
39. Smith H.O., Hutchison III C.A., Pfannkoch C., and Venter J.C. Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc. Natl. Acad. Sci. USA 100 (2003) 15440-15445
40. Soll D., Ohtsuka E., Jones D.S., Lohrmann R., Hayatsu H., Nishimura S., and Khorana H.G. Studies on polynucleotides, XLIX. Stimulation of the binding of aminoacyl-sRNA's to ribosomes by ribotrinucleotides and a survey of codon assignments for 20 amino acids. Proc. Natl. Acad. Sci. USA 54 (1965) 1378-1385
41. Stemmer W.P., Crameri A., Ha K.D., Brennan T.M., and Heyneker H.L. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene 164 (1995) 49-53
42. Takehisa J., Kraus M.H., Decker J.M., Li Y., Keele B.F., Bibollet-Ruche F., Zammit K.P., Weng Z., Santiago M.L., Kamenya S., et al. Generation of infectious molecular clones of simian immunodeficiency virus from fecal consensus sequences of wild chimpanzees. J. Virol. 81 (2007) 7463-7475
43. Taubenberger J.K., Reid A.H., Krafft A.E., Bijwaard K.E., and Fanning T.G. Initial genetic characterization of the 1918 "Spanish" influenza virus. Science 275 (1997) 1793-1796
44. Tian J., Gong H., Sheng N., Zhou X., Gulari E., Gao X., and Church G. Accurate multiplex gene synthesis from programmable DNA microchips. Nature 432 (2004) 1050-1054
45. Tumpey T.M., Basler C.F., Aguilar P.V., Zeng H., Solorzano A., Swayne D.E., Cox N.J., Katz J.M., Taubenberger J.K., Palese P., and Garcia-Sastre A. Characterization of the reconstructed 1918 Spanish influenza pandemic virus. Science 310 (2005) 77-80
46. WHO. Fact Sheet No. 211-Influenza (2003), World Health Organization, Geneva
47. Young L., and Dong Q. Two-step total gene synthesis method. Nucleic Acids Res. 32 (2004) e59
48. Zolotukhin S., Potter M., Hauswirth W.W., Guy J., and Muzyczka N. A "humanized" green fluorescent protein cDNA adapted for high-level expression in mammalian cells. J. Virol. 70 (1996) 4646-4654