Model-driven engineering of gene expression from RNA replicons

ACS Synthetic Biology

Volumn 4, Issue 1, 2015, Pages 48-56

  Beal, Jacob ^a   Wagner, Tyler E ^b   Kitada, Tasuku ^c   Azizgolshani, Odisse ^d   Parker, Jordan Moberg ^d   Densmore, Douglas ^b   Weiss, Ron ^c  

^a BBN TECHNOLOGIES   (United States)

^b BOSTON UNIVERSITY   (United States)

^c Massachusetts Institute of Technology Cambridge   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Alphavirus; Circuit prediction; Expression control; Flow cytometry; Quantitative modeling; Replicon; Sindbis; TASBE characterization

Indexed keywords

RNA; PHOTOPROTEIN; VIRUS RNA;

ANIMAL CELL; ARTICLE; COMPUTER MODEL; CONTROLLED STUDY; ERROR; GENE EXPRESSION; GENETIC ENGINEERING; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; REPLICON; SINDBIS VIRUS; TITRIMETRY; ANIMAL; BIOLOGICAL MODEL; CELL LINE; GENETIC TRANSFECTION; GENETICS; HAMSTER; PROCEDURES; SYNTHETIC BIOLOGY;

ALPHAVIRUS; CRICETINAE; SINDBIS VIRUS;

ANIMALS; CELL LINE; CRICETINAE; GENE EXPRESSION; GENETIC ENGINEERING; LUMINESCENT PROTEINS; MODELS, GENETIC; REPLICON; RNA, VIRAL; SINDBIS VIRUS; SYNTHETIC BIOLOGY; TRANSFECTION;

EID: 84921395938     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb500173f     Document Type: Article

References (42)

1. Lundstrom, K. (2009) Alphaviruses in Gene Therapy. Viruses 1, 13-25.
2. Lundstrom, K. (2012) Alphavirus Vectors in Vaccine Development. J. Vaccines Vaccin. 3 DOI: 10.4172/2157-7560.1000139.
3. Wahlfors, J. J., Zullo, S. A., Loimas, S., Nelson, D. M., and Morgan, R. A. (2000) Evaluation of recombinant alphaviruses as vectors in gene therapy. Gene Ther. 7, 472 DOI: 101038sjgt3301122.
4. Yoshioka, N., Gros, E., Li, H.-R., Kumar, S., Deacon, D. C., Maron, C., Muotri, A. R., Chi, N. C., Fu, X.-D., Yu, B. D., and Dowdy, S. F. (2013) Efficient generation of human iPSCs by a synthetic self-replicative RNA. Cell Stem Cell 13, 246-254.
5. Xiong, C., Levis, R., Shen, P., Schlesinger, S., Rice, C. M., and Huang, H. V. (1989) Sindbis virus: An efficient, broad host range vector for gene expression in animal cells. Science 243, 1188-1191.
6. Kulasegaran-Shylini, R., Thiviyanathan, V., Gorenstein, D. G., and Frolov, I. (2009) The 5′UTR-specific mutation in VEEV TC-83 genome has a strong effect on RNA replication and subgenomic RNA synthesis, but not on translation of the encoded proteins. Virology 387, 211-221.
7. Kouprina, N., Earnshaw, W. C., Masumoto, H., and Larionov, V. (2013) A new generation of human artificial chromosomes for functional genomics and gene therapy. Cell. Mol. Life Sci. CMLS 70, 1135-1148.
8. Robertson, J. S. (1994) Safety considerations for nucleic acid vaccines. Vaccine 12, 1526-1528.
9. Klinman, D. M., Takeno, M., Ichino, M., Gu, M., Yamshchikov, G., Mor, G., and Conover, J. (1997) DNA vaccines: Safety and efficacy issues. Springer Semin. Immunopathol. 19, 245-256.
10. Frolov, I., Agapov, E., Hoffman, T. A., Prágai, B. M., Lippa, M., Schlesinger, S., and Rice, C. M. (1999) Selection of RNA replicons capable of persistent noncytopathic replication in mammalian cells. J. Virol. 73, 3854-3865.
11. Lustig, S., Jackson, A. C., Hahn, C. S., Griffin, D. E., Strauss, E. G., and Strauss, J. H. (1988) Molecular basis of Sindbis virus neurovirulence in mice. J. Virol. 62, 2329-2336.
12. Heise, M. T., White, L. J., Simpson, D. A., Leonard, C., Bernard, K. A., Meeker, R. B., and Johnston, R. E. (2003) An attenuating mutation in nsP1 of the Sindbis-group virus S.A.AR86 accelerates nonstructural protein processing and up-regulates viral 26S RNA synthesis. J. Virol. 77, 1149-1156.
13. Dryga, S. A., Dryga, O. A., and Schlesinger, S. (1997) Identification of mutations in a Sindbis virus variant able to establish persistent infection in BHK Cells: The importance of a mutation in the nsP2 gene. Virology 228, 74-83.
14. Perri, S., Driver, D. A., Gardner, J. P., Sherrill, S., Belli, B. A., Dubensky, T. W., and Polo, J. M. (2000) Replicon vectors derived from Sindbis virus and Semliki Forest virus that establish persistent replication in host cells. J. Virol. 74, 9802-9807.
15. Strauss, J. H., and Strauss, E. G. (1994) The alphaviruses: Gene expression, replication, and evolution. Microbiol. Rev. 58, 491-562.
16. Hardy, W. R., and Strauss, J. H. (1989) Processing the nonstructural polyproteins of sindbis virus: Nonstructural proteinase is in the C-terminal half of nsP2 and functions both in cis and in trans. J. Virol. 63, 4653-4664.
17. Shirako, Y., and Strauss, J. H. (1990) Cleavage between nsP1 and nsP2 initiates the processing pathway of Sindbis virus nonstructural polyprotein P123. Virology 177, 54-64.
18. Jose, J., Snyder, J. E., and Kuhn, R. J. (2009) A structural and functional perspective of alphavirus replication and assembly. Future Microbiol. 4, 837-856.
19. Schlesinger, S., and Dubensky, T. W., Jr. (1999) Alphavirus vectors for gene expression and vaccines. Curr. Opin. Biotechnol. 10, 434-439.
20. Agapov, E. V., Frolov, I., Lindenbach, B. D., Pragai, B. M., Schlesinger, S., and Rice, C. M. (1998) Noncytopathic Sindbis virus RNA vectors for heterologous gene expression. Proc. Natl. Acad. Sci. U.S.A. 95, 12989-12994.
21. Geall, A. J., Verma, A., Otten, G. R., Shaw, C. A., Hekele, A., Banerjee, K., Cu, Y., Beard, C. W., Brito, L. A., Krucker, T., O'Hagan, D. T., Singh, M., Mason, P. W., Valiante, N. M., Dormitzer, P. R., Barnett, S. W., Rappuoli, R., Ulmer, J. B., and Mandl, C. W. (2012) Nonviral delivery of self-amplifying RNA vaccines. Proc. Natl. Acad. Sci. U.S.A. 109, 14604-14609.
22. Hahn, C. S., Hahn, Y. S., Braciale, T. J., and Rice, C. M. (1992) Infectious Sindbis virus transient expression vectors for studying antigen processing and presentation. Proc. Natl. Acad. Sci. U.S.A. 89, 2679-2683.
23. Frolov, I., Hoffman, T. A., Pragai, B. M., Dryga, S. A., Huang, H. V., Schlesinger, S., and Rice, C. M. (1996) Alphavirus-based expression vectors: Strategies and applications. Proc. Natl. Acad. Sci. U.S.A. 93, 11371-11377.
24. Petrakova, O., Volkova, E., Gorchakov, R., Paessler, S., Kinney, R. M., and Frolov, I. (2005) Noncytopathic replication of venezuelan equine encephalitis virus and eastern equine encephalitis virus replicons in mammalian cells. J. Virol. 79, 7597-7608.
25. Wiley, M. R., Roberts, L. O., Adelman, Z. N., Myles, K. M. (2010) Double subgenomic alphaviruses expressing multiple fluorescent proteins using a Rhopalosiphum padi virus internal ribosome entry site element. PLoS One 5.
26. Sanz, M. Á., Castelló, A., Ventoso, I., Berlanga, J. J., and Carrasco, L. (2009) Dual Mechanism for the Translation of Subgenomic mRNA from Sindbis Virus in Infected and Uninfected Cells. PLoS One 4, e4772.
27. Firth, A. E., and Brierley, I. (2012) Non-canonical translation in RNA viruses. J. Gen. Virol. 93, 1385-1409.
28. Donnelly, M. L. L., Luke, G., Mehrotra, A., Li, X., Hughes, L. E., Gani, D., and Ryan, M. D. (2001) Analysis of the aphthovirus 2A/2B polyprotein "cleavage" mechanism indicates not a proteolytic reaction, but a novel translational effect: A putative ribosomal "skip. J. Gen. Virol. 82, 1013-1025.
29. Thomas, J. M., Klimstra, W. B., Ryman, K. D., and Heidner, H. W. (2003) Sindbis virus vectors designed to express a foreign protein as a cleavable component of the viral structural polyprotein. J. Virol. 77, 5598-5606.
30. Kim, J. H., Lee, S.-R., Li, L.-H., Park, H.-J., Park, J.-H., Lee, K. Y., Kim, M.-K., Shin, B. A., Choi, S.-Y. (2011) High cleavage efficiency of a 2A peptide derived from porcine teschovirus-1 in human cell lines, zebrafish, and mice. PLoS One 6.
31. Frolov, I., and Schlesinger, S. (1994) Translation of Sindbis virus mRNA: Effects of sequences downstream of the initiating codon. J. Virol. 68, 8111-8117.
32. Caley, I. J., Betts, M. R., Davis, N. L., Swanstrom, R., Frelinger, J. A., and Johnston, R. E. (1999) Venezuelan equine encephalitis virus vectors expressing HIV-1 proteins: Vector design strategies for improved vaccine efficacy. Vaccine 17, 3124-3135.
33. Kallio, K., Hellström, K., Balistreri, G., Spuul, P., Jokitalo, E., and Ahola, T. (2013) Template RNA length determines the size of replication complex spherules for Semliki Forest virus. J. Virol. 87, 9125-9134.
34. Decker, C. J., and Parker, R. (2012) P-bodies and stress granules: Possible roles in the control of translation and mRNA degradation. Cold Spring Harb. Perspect. Biol. 4, a012286.
35. Wengler, G., Koschinski, A., Wengler, G., and Dreyer, F. (2003) Entry of alphaviruses at the plasma membrane converts the viral surface proteins into an ion-permeable pore that can be detected by electrophysiological analyses of whole-cell membrane currents. J. Gen. Virol. 84, 173-181.
36. Paul, D., and Bartenschlager, R. (2013) Architecture and biogenesis of plus-strand RNA virus replication factories. World J. Virol. 2, 32-48.
37. Perri, S., Greer, C. E., Thudium, K., Doe, B., Legg, H., Liu, H., Romero, R. E., Tang, Z., Bin, Q., Dubensky, T. W., Vajdy, M., Otten, G. R., and Polo, J. M. (2003) An alphavirus replicon particle chimera derived from venezuelan equine encephalitis and sindbis viruses is a potent gene-based vaccine delivery vector. J. Virol. 77, 10394-10403.
38. Mahmoud, H. (2008) Polya Urn Models. CRC Press, Boca Raton, FL.
39. Petrakova, O., Volkova, E., Gorchakov, R., Paessler, S., Kinney, R. M., and Frolov, I. (2005) Noncytopathic replication of Venezuelan equine encephalitis virus and eastern equine encephalitis virus replicons in Mammalian cells. J. Virol. 79, 7597-7608.
40. Azizgolshani, O., Garmann, R. F., Cadena-Nava, R., Knobler, C. M., and Gelbart, W. M. (2013) Reconstituted plant viral capsids can release genes to mammalian cells. Virology 441, 12-17.
41. Beal, J.; Weiss, R.; Yaman, F.; Davidsohn, N.; Adler, A. A Method for Fast, High-Precision Characterization of Synthetic Biology Devices; Computer Science and Artificial Intelligence Laboratory Technical Report; MIT: Cambridge, MA, 2012
42. Perfetto, S. P., Ambrozak, D., Nguyen, R., Chattopadhyay, P., and Roederer, M. (2006) Quality assurance for polychromatic flow cytometry. Nat. Protoc. 1, 1522-1530.