Intrinsic biocontainment: Multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 6, 2015, Pages 1803-1808

  Cai, Yizhi ^a,b   Agmon, Neta ^b,c   Choi, Woo Jin ^b   Ubide, Alba ^a   Stracquadanio, Giovanni ^b,d   Caravelli, Katrina ^b   Hao, Haiping ^b   Bader, Joel S ^b,d   Boeke, Jef D ^b,c  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c NEW YORK UNIVERSITY MEDICAL CENTER   (United States)

^d Johns Hopkins University   (United States)

Author keywords

Biosafety; Biotechnology; Saccharomyces cerevisiae

Indexed keywords

CRE RECOMBINASE; ESTRADIOL; FUNGAL ENZYME; FUNGAL PROTEIN; HISTONE; HISTONE H3; HISTONE H4; RECOMBINASE; TRANSCRIPTOME;

ARTICLE; BIOCONTAINMENT; CONTROLLED STUDY; DAUGHTER CELL; ENZYME ACTIVITY; ESSENTIAL GENE; ESTROGEN BINDING; FUNGUS GROWTH; GENE FUNCTION; GENE SWITCHING; GENETIC ENGINEERING; GENETIC RECOMBINATION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION REGULATION; BIOTECHNOLOGY; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; GENETICS; GROWTH, DEVELOPMENT AND AGING; HAZARDOUS WASTE; METABOLISM; MUTATION; PROCEDURES; TRANSGENIC ORGANISM;

SACCHAROMYCES CEREVISIAE;

BIOTECHNOLOGY; CONTAINMENT OF BIOHAZARDS; GENE EXPRESSION PROFILING; GENES, ESSENTIAL; GENETIC ENGINEERING; MUTATION; ORGANISMS, GENETICALLY MODIFIED; RECOMBINASES; RECOMBINATION, GENETIC; SACCHAROMYCES CEREVISIAE; TRANSCRIPTION, GENETIC;

EID: 84922678329     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1424704112     Document Type: Article

References (40)

1. Way JC, Collins JJ, Keasling JD, Silver PA (2014) Integrating biological redesign: Where synthetic biology came from and where it needs to go. Cell 157(1):151-161.
2. Cello J, Paul AV, Wimmer E (2002) Chemical synthesis of poliovirus cDNA: Generation of infectious virus in the absence of natural template. Science 297(5583):1016-1018.
3. Lee YN, Bieniasz PD (2007) Reconstitution of an infectious human endogenous retrovirus. PLoS Pathog 3(1):e10.
4. 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(26):15440-15445.
5. Tumpey TM, et al. (2005) Characterization of the reconstructed 1918 Spanish influenza pandemic virus. Science 310(5745):77-80.
6. Gibson DG, et al. (2008) Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319(5867):1215-1220.
7. Gibson DG, et al. (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329(5987):52-56.
8. Annaluru N, et al. (2014) Total synthesis of a functional designer eukaryotic chromosome. Science 344(6179):55-58.
9. Dymond JS, et al. (2011) Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature 477(7365):471-476.
10. Ellis T, Adie T, Baldwin GS (2011) DNA assembly for synthetic biology: From parts to pathways and beyond. Integr Biol (Camb) 3(2):109-118.
11. Isaacs FJ, et al. (2011) Precise manipulation of chromosomes in vivo enables genomewide codon replacement. Science 333(6040):348-353.
12. Wang HH, et al. (2009) Programming cells by multiplex genome engineering and accelerated evolution. Nature 460(7257):894-898.
13. 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(20):2760-2767.
14. Czar MJ, Cai Y, Peccoud J (2009) Writing DNA with GenoCAD. Nucleic Acids Res 37(Web Server issue):W40-W47.
15. Hillson NJ, Rosengarten RD, Keasling JD (2012) j5 DNA assembly design automation software. ACS Synth Biol 1(1):14-21.
16. Moe-Behrens GH, Davis R, Haynes KA (2013) Preparing synthetic biology for the world. Front Microbiol 4:5.
17. Frank KM, Schneewind O, Shieh WJ (2011) Investigation of a researcher's death due to septicemic plague. N Engl J Med 364(26):2563-2564.
18. Bej AK, Perlin MH, Atlas RM (1988) Model suicide vector for containment of genetically engineered microorganisms. Appl Environ Microbiol 54(10):2472-2477.
19. Gerdes K, et al. (1986) Mechanism of postsegregational killing by the hok gene product of the parB system of plasmid R1 and its homology with the relF gene product of the E. coli relB operon. EMBO J 5(8):2023-2029.
20. Knudsen SM, Karlström OH (1991) Development of efficient suicide mechanisms for biological containment of bacteria. Appl Environ Microbiol 57(1):85-92.
21. Poulsen LK, Larsen NW, Molin S, Andersson P (1989) A family of genes encoding a cellkilling function may be conserved in all gram-negative bacteria. Mol Microbiol 3(11): 1463-1472.
22. Wright O, Delmans M, Stan G-B, Ellis T (2014) GeneGuard: A modular plasmid system designed for biosafety. ACS Synth Biol, 10.1021/sb500234s.
23. Dai J, et al. (2008) Probing nucleosome function: A highly versatile library of synthetic histone H3 and H4 mutants. Cell 134(6):1066-1078.
24. Sikorski RS, Hieter P (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics 122(1):19-27.
25. Lea DE, Coulson CA (1949) The distribution of the numbers of mutants in bacterial populations. J Genet 49(3):264-285.
26. McIsaac RS, et al. (2011) Fast-acting and nearly gratuitous induction of gene expression and protein depletion in Saccharomyces cerevisiae. Mol Biol Cell 22(22): 4447-4459.
27. Lindstrom DL, Gottschling DE (2009) The mother enrichment program: A genetic system for facile replicative life span analysis in Saccharomyces cerevisiae. Genetics 183(2):413-422, 1SI-13SI.
28. Engler C, Gruetzner R, Kandzia R, Marillonnet S (2009) Golden Gate shuffling: A onepot DNA shuffling method based on type IIs restriction enzymes. PLoS One 4(5):e5553.
29. Moilanen A, Rouleau N, Ikonen T, Palvimo JJ, Jänne OA (1997) The presence of a transcription activation function in the hormone-binding domain of androgen receptor is revealed by studies in yeast cells. FEBS Lett 412(2):355-358.
30. Popovic N, et al. (2010) Site-specific and dose-dependent effects of glucocorticoid receptor phosphorylation in yeast Saccharomyces cerevisiae. Steroids 75(6):457-465.
31. Wang Y, O'Malley BW, Jr, Tsai SY, O'Malley BW (1994) A regulatory system for use in gene transfer. Proc Natl Acad Sci USA 91(17):8180-8184.
32. Gallagher RR, Patel JR, Interiano AL, Rovner AJ, Isaacs FJ (2015) Multilayered genetic safeguards limit growth of microorganisms to defined environments. Nucleic Acids Res, 10.1093/nar/gku1378.
33. Rovner AJ, et al. (2015) Recoded organisms engineered to depend on synthetic amino acids. Nature, 10.1038/nature14095.
34. Schiestl RH, Gietz RD (1989) High efficiency transformation of intact yeast cells using single stranded nucleic acids as a carrier. Curr Genet 16(5-6):339-346.
35. Boeke JD, Trueheart J, Natsoulis G, Fink GR (1987) 5-Fluoroorotic acid as a selective agent in yeast molecular genetics. Methods Enzymol 154:164-175.
36. Vidal M, Brachmann RK, Fattaey A, Harlow E, Boeke JD (1996) Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc Natl Acad Sci USA 93(19):10315-10320.
37. Kim D, et al. (2013) TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14(4):R36.
38. Anders S, Pyl PT, Huber W (2014) HTSeq-a Python framework to work with highthroughput sequencing data. Bioinformatics 31(2):166-169.
39. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11(10):R106.
40. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc B 57(1):289-300.