Synthetic bugs on the loose: Containment options for deeply engineered (micro)organisms

Current Opinion in Biotechnology

Volumn 38, Issue , 2016, Pages 90-96

  Schmidt, Markus ^a   de Lorenzo, Víctor ^b  

^a Biofaction KG   (Austria)

^b CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTECHNOLOGY;

ENVIRONMENTAL FATE; GENETIC CIRCUITS; GENETIC CODE; GENETIC MODIFICATIONS; HORIZONTAL GENE TRANSFER; SYNTHETIC BIOLOGY;

GENE TRANSFER;

AMINO ACID; NUCLEOTIDE; XENOBIOTIC AGENT;

BIOTECHNOLOGY; DNA MODIFICATION; ENVIRONMENTAL IMPACT; ESCHERICHIA COLI; GALLERIA MELLONELLA; GENOME; HORIZONTAL GENE TRANSFER; NONHUMAN; PRIORITY JOURNAL; REVIEW; RISK ASSESSMENT; STAPHYLOCOCCUS AUREUS; SURVIVAL; SYNTHETIC BIOLOGY; TRANSGENIC ORGANISM; ANIMAL; HAZARDOUS WASTE; HUMAN; PROCEDURES; RISK FACTOR;

ANIMALS; BIOTECHNOLOGY; CONTAINMENT OF BIOHAZARDS; HUMANS; RISK FACTORS; SYNTHETIC BIOLOGY;

EID: 84957806669     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2016.01.006     Document Type: Review

References (77)

1. Berg P., Baltimore D., Brenner S., Roblin R.O., Singer M.F. Asilomar conference on recombinant DNA molecules. Science 1975, 188:991-994.
2. Berg P., Baltimore D., Brenner S., Roblin R.O., Singer M.F. Summary statement of the Asilomar conference on recombinant DNA molecules. Proc Natl Acad Sci U S A 1975, 72:1981-1984.
3. Watson J.D., Tooze J. The DNA Story, A Documentary History of Gene Cloning 1981, Freeman.
4. Chakrabarty A. Genetically-manipulated microorganisms and their products in the oil service industries. Trends Biotech 1985, 3:32-39.
5. Rojo F., Pieper D.H., Engesser K.-H., Knackmuss H.-J., Timmis K.N. Assemblage of ortho cleavage route for simultaneous degradation of chloro- and methylaromatics. Science 1987, 238:1395-1398.
6. Ramos J.L., Andersson P., Jensen L.B., Ramos C., Ronchel M.C., Diaz E., Timmis K.N., Molin S. Suicide microbes on the loose. Biotechnology (NY) 1995, 13:35-37.
7. de Lorenzo V. Environmental biosafety in the age of synthetic biology: do we really need a radical new approach?. Bioessays 2010, 32:926-931.
8. Schmidt M., de Lorenzo V. Synthetic constructs in/for the environment: managing the interplay between natural and engineered biology. FEBS Lett 2012, 586:2199-2206.
9. Cases I., de Lorenzo V. Genetically modified organisms for the environment: stories of success and failure and what we have learned from them. Int Microbiol 2005, 8:213-222.
10. Lindow S., Panopoulos N., McFarland B. Genetic engineering of bacteria from managed and natural habitats. Science 1989, 244:1300-1307.
11. Endy D. Foundations for engineering biology. Nature 2005, 438:449-453.
12. Andrianantoandro E., Basu S., Karig D.K., Weiss R. Synthetic biology: new engineering rules for an emerging discipline. Mol Sys Biol 2006, 2.
13. de Lorenzo V., Danchin A. Synthetic biology: discovering new worlds and new words. EMBO Rep 2008, 9:822-827.
14. Acevedo-Rocha C.G. The synthetic nature of biology. Ambivalences of Creating Life 2016, Springer, pp 9-53.
15. Porcar M., Danchin A., de Lorenzo V. Confidence, tolerance, and allowance in biological engineering: the nuts and bolts of living things. Bioessays 2015, 37:95-102.
16. Schmidt M. Xenobiology: a new form of life as the ultimate biosafety tool. Bioessays 2010, 32:322-331.
17. Schmidt M. Safeguarding the genetic firewall with xenobiology. 21st Century Borders/Synthetic Biology: Focus on Responsibility and Governance 2012, 55. Institute on Science for Global Policy.
18. Acevedo-Rocha C.G., Schulze-Makuch D. How many biochemistries are available to build a cell?. Chembiochem 2015, 16:2137-2139.
19. Marliere P. The farther, the safer: a manifesto for securely navigating synthetic species away from the old living world. Syst Synth Biol 2009, 3:77-84.
20. Moe-Behrens G.H., Davis R., Haynes K.A. Preparing synthetic biology for the world. Front Microbiol 2013, 4:5.
21. Risks SCoEaNIH Opinion on Synthetic Biology I. Definition 2014, European Commission.
22. Risks SCoEaNIH Opinion on Synthetic Biology II. Risk Assessment Methodologies and Safety Aspects 2015, European Commission.
23. Risks SCoEaNIH Final Opinion on Synthetic Biology III: Risks to the Environment and Biodiversity Related to Synthetic Biology and Research Priorities in the Field of Synthetic Biology 2015, European Commission.
24. Redford K.H., Adams W., Mace G.M. Synthetic biology and conservation of nature: wicked problems and wicked solutions. PLoS Biol 2013, 11:e1001530.
25. Alphey L., Alphey N. Five things to know about genetically modified (GM) insects for vector control. PLoS Pathog 2014, 10:e1003909.
26. Carmichael R.E., Boyce A., Matthewman C., Patron N.J. An introduction to synthetic biology in plant systems. New Phytol 2015, 208:20-22.
27. Patron N.J., Orzaez D., Marillonnet S., Warzecha H., Matthewman C., Youles M., Raitskin O., Leveau A., Farré G., Rogers C. Standards for plant synthetic biology: a common syntax for exchange of DNA parts. New Phytol 2015, 208:13-19.
28. Zhang Y., Chen J., Cui X., Luo D., Xia H., Dai J., Zhu Z., Hu W. A controllable on-off strategy for the reproductive containment of fish. Sci Rep 2015, 5:7614.
29. Alphey L. Genetic control of mosquitoes. Annu Rev Entomol 2014, 59:205-224.
30. Gantz V.M., Jasinskiene N. Highly efficient Cas9-mediated gene drive for population modification of the malaria vector mosquito Anopheles stephensi. Proc Natl Acad Sci U S A 2015, 112:6736-6743.
31. Hammond A., Galizi R. A CRISPR-Cas9 gene drive system targeting female reproduction in the malaria mosquito vector Anopheles gambiae. Nat Biotechnol 2016, 34:78-83.
32. Harris A.F., Nimmo D., McKemey A.R., Kelly N., Scaife S., Donnelly C.A., Beech C., Petrie W.D., Alphey L. Field performance of engineered male mosquitoes. Nat Biotechnol 2011, 29:1034-1037.
33. Lacroix R., McKemey A.R., Raduan N., Kwee Wee L., Hong Ming W., Guat Ney T., Rahidah A.A.S., Salman S., Subramaniam S., Nordin O., et al. Open field release of genetically engineered sterile male Aedes aegypti in Malaysia. PLoS One 2012, 7:e42771.
34. Lajoie M.J., Rovner A.J., Goodman D.B., Aerni H.R., Haimovich A.D., Kuznetsov G., Mercer J.A., Wang H.H., Carr P.A., Mosberg J.A., et al. Genomically recoded organisms expand biological functions. Science 2013, 342:357-360.
35. Mandell D.J., Lajoie M.J., Mee M.T., Takeuchi R., Kuznetsov G., Norville J.E., Gregg C.J., Stoddard B.L., Church G.M. Biocontainment of genetically modified organisms by synthetic protein design. Nature 2015, 518:55-60.
36. Rovner A.J., Haimovich A.D., Katz S.R., Li Z., Grome M.W., Gassaway B.M., Amiram M., Patel J.R., Gallagher R.R., Rinehart J., et al. Recoded organisms engineered to depend on synthetic amino acids. Nature 2015, 518:89-93.
37. Marliere P., Patrouix J., Doring V., Herdewijn P., Tricot S., Cruveiller S., Bouzon M., Mutzel R. Chemical evolution of a bacterium's genome. Angew Chem Int Ed Engl 2011, 50:7109-7114.
38. Pezo V., Liu F.W., Abramov M., Froeyen M., Herdewijn P., Marliere P. Binary genetic cassettes for selecting XNA-templated DNA synthesis in vivo. Angew Chem Int Ed Engl 2013, 52:8139-8143.
39. Malyshev D.A., Dhami K., Lavergne T., Chen T., Dai N., Foster J.M., Correa I.R., Romesberg F.E. A semi-synthetic organism with an expanded genetic alphabet. Nature 2014, 509:385-388.
40. Malyshev D.A., Romesberg F.E. The expanded genetic alphabet. Angew Chem Int Ed Engl 2015, 54:11930-11944.
41. Mimee M., Tucker A.C., Voigt C.A., Lu T.K. Programming a human commensal bacterium, Bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota. Cell Systems 2015, 1:62-71.
42. de Lorenzo V. Exploiting microbial diversity: the challenges and the means. Handbook of Hydrocarbon and Lipid Microbiology 2010, Springer, pp 2435-2458.
43. Sole R.V., Montanez R., Duran-Nebreda S. Synthetic circuit designs for earth terraformation. Biol Direct 2015, 10:37.
44. Landrain T., Meyer M., Perez A.M., Sussan R. Do-it-yourself biology: challenges and promises for an open science and technology movement. Sys Synth Biol 2013, 7:115-126.
45. Seyfried G., Pei L., Schmidt M. European do-it-yourself (DIY) biology: beyond the hope, hype and horror. Bioessays 2014, 36:548-551.
46. Grushkin D., Kuilen T., Millet P. Seven Myths and Realities about Do-It-Yourself Biology 2013, Wilson Centre.
47. Taleb NN, Read R, Douady R, Norman J, Bar-Yam Y: The precautionary principle (with application to the genetic modification of organisms). arXiv preprint: arXiv 1410.5787 2014.
48. Carter S.R., Rodemeyer M., Garfinkel M.S., Friedman R.M. Synthetic Biology and the US Biotechnology Regulatory System: Challenges and Options 2014, J. Craig Venter Institute.
49. Palmer M.J., Fukuyama F., Relman D.A. A more systematic approach to biological risk. Science 2015, 350:1471-1473.
50. Ravikumar A., Liu C.C. Biocontainment through reengineered genetic codes. Chembiochem 2015, 16:1149-1151.
51. Henry A.A., Romesberg F.E. Beyond A, C G and T: augmenting nature's alphabet. Curr Opin Chem Biol 2003, 7:727-733.
52. Davis L., Chin J.W. Designer proteins: applications of genetic code expansion in cell biology. Nat Rev Mol Cell Biol 2012, 13:168-182.
53. Wang K., Schmied W.H., Chin J.W. Reprogramming the genetic code: from triplet to quadruplet codes. Angew Chem Int Ed Engl 2012, 51:2288-2297.
54. Wright O., Delmans M., Stan G.B., Ellis T. GeneGuard: a modular plasmid system designed for biosafety. ACS Synth Biol 2015, 4:307-316.
55. Gallagher R.R., Patel J.R., Interiano A.L., Rovner A.J., Isaacs F.J. Multilayered genetic safeguards limit growth of microorganisms to defined environments. Nucleic Acids Res 2015, 43:1945-1954.
56. Chan C.T., Lee J.W., Cameron D.E., Bashor C.J., Collins J.J. 'Deadman' and 'Passcode' microbial kill switches for bacterial containment. Nat Chem Biol 2016, 12:82-86.
57. Cai Y., Agmon N., Choi W.J., Ubide A., Stracquadanio G., Caravelli K., Hao H., Bader J.S., Boeke J.D. Intrinsic biocontainment: multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes. Proc Natl Acad Sci U S A 2015, 112:1803-1808.
58. Wang X.J., Jin X., Dun B.Q., Kong N., Jia S.R., Tang Q.L., Wang Z.X. Gene-splitting technology: a novel approach for the containment of transgene flow in Nicotiana tabacum. PLoS One 2014, 9:e99651.
59. Ledford H. Transgenic salmon nears approval. Nature 2013, 497:17-18.
60. Gantz V.M., Bier E. Genome editing. The mutagenic chain reaction: a method for converting heterozygous to homozygous mutations. Science 2015, 348:442-444.
61. Esvelt K.M., Smidler A.L., Catteruccia F., Church G.M. Concerning RNA-guided gene drives for the alteration of wild populations. eLife 2014, e03401.
62. Webber B.L., Raghu S., Edwards O.R. Opinion: is CRISPR-based gene drive a biocontrol silver bullet or global conservation threat?. Proc Natl Acad Sci U S A 2015, 112:10565-10567.
63. Oye K.A., Esvelt K., Appleton E., Catteruccia F., Church G., Kuiken T., Lightfoot S.B., McNamara J., Smidler A., Collins J.P. Regulating gene drives. Science 2014, 345:626-628.
64. Akbari O.S., Bellen H.J., Bier E., Bullock S.L., Burt A., Church G.M., Cook K.R., Duchek P., Edwards O.R., Esvelt K.M., et al. Safeguarding gene drive experiments in the laboratory. Science 2015, 349:927-929.
65. DiCarlo J.E., Chavez A., Dietz S.L., Esvelt K.M. Safeguarding CRISPR-Cas9 gene drives in yeast. Nat Biotech 2015, 33:1250-1255.
66. Citorik R.J., Mimee M., Lu T.K. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. Nat Biotechnol 2014, 32:1141-1145.
67. Bikard D., Euler C.W., Jiang W., Nussenzweig P.M., Goldberg G.W., Duportet X., Fischetti V.A., Marraffini L.A. Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials. Nat Biotechnol 2014, 32:1146-1150.
68. Yosef I., Manor M., Kiro R., Qimron U. Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria. Proc Natl Acad Sci U S A 2015, 112:7267-7272.
69. Ando H., Lemire S., Pires D.P., Lu T.K. Engineering modular viral scaffolds for targeted bacterial population editing. Cell Systems 2015, 1:187-196.
70. Brüssow H. Editorial commentary: phage therapy: quo vadis?. Clin Infect Dis 2014, 58:535-536.
71. Withey S., Cartmell E., Avery L.M., Stephenson T. Bacteriophages - potential for application in wastewater treatment processes. Sci Total Environ 2005, 339:1-18.
72. Wang W., Li M., Li Y. Intervention strategies for reducing Vibrio parahaemolyticus in seafood: a review. J Food Sci 2015, 80:10-19.
73. Zaczek M., Weber-Dabrowska B., Gorski A. Phages in the global fruit and vegetable industry. J Appl Microbiol 2015, 118:537-556.
74. Lu T.K., Koeris M.S. The next generation of bacteriophage therapy. Curr Opin Microbiol 2011, 14:524-531.
75. Krom R.J., Bhargava P., Lobritz M.A., Collins J.J. Engineered phagemids for nonlytic, targeted antibacterial therapies. Nano Lett 2015, 15:4808-4813.
76. Garcia J.L., Diaz E. Plasmids as tools for containment. Microbiol Spectr 2014, 2.
77. Schmidt M., Pei L. Synthetic toxicology: where engineering meets biology and toxicology. Toxicol Sci 2011, 120(Suppl. 1):S204-S224.