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Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression

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Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression

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Shen, S.; Rodrigo Tarrega, G.; Prakash, S.; Majer, E.; Landrain, T.; Kirov, B.; Daros Arnau, JA.... (2015). Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression. Nucleic Acids Research. 43(10):5158-5170. https://doi.org/10.1093/nar/gkv287

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/66174

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Título: Dynamic signal processing by ribozyme-mediated RNA circuits to control gene expression
Autor: Shen, Shensi Rodrigo Tarrega, Guillermo Prakash, Satya Majer, Eszter Landrain, T.E. Kirov, Boris Daros Arnau, Jose Antonio Jaramillo, Alfonso
Entidad UPV: Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes
Fecha difusión:
Resumen:
[EN] Organisms have different circuitries that allow converting signal molecule levels to changes in gene expression. An important challenge in synthetic biology involves the de novo design of RNA modules enabling dynamic ...[+]
Palabras clave: RNA , Synthetic biology , Computational design , Automated design , Living cells , Riboregulators , Platform , Systems , Protein , Transduction , Degradation
Derechos de uso: Reconocimiento (by)
Fuente:
Nucleic Acids Research. (issn: 0305-1048 ) (eissn: 1362-4962 )
DOI: 10.1093/nar/gkv287
Editorial:
Oxford University Press (OUP)
Versión del editor: https://dx.doi.org/10.1093/nar/gkv287
Código del Proyecto:
info:eu-repo/grantAgreement/MICINN//BIO2011-26741/ES/PATOGENOS DE RNA DE PLANTAS: INTERACCION CON EL HUESPED Y DESARROLLO DE HERRAMIENTAS BIOTECNOLOGICAS/
info:eu-repo/grantAgreement/EC/FP7/610730/EU/General-Purpose Programmable Evolution Machine on a Chip/
info:eu-repo/grantAgreement/EC//ALTF-1177-2011/
info:eu-repo/grantAgreement/EC/FP7/613745/EU/Programming synthetic networks for bio-based production of value chemicals/
info:eu-repo/grantAgreement/MECD//AP2012-3751/ES/AP2012-3751/
Agradecimientos:
EVOPROG [FP7-ICT-610730]; PROMYS [FP7-KBBE-613745 to A.J.]; Ministerio de Economia y Competitividad, Spain [BIO2011-26741 to J.-A.D.]; PRES Paris Sud grant (S.S.); EMBO long-term fellowship co-funded by Marie Curie actions ...[+]
Tipo: Artículo

References

Ulrich, L. E., Koonin, E. V., & Zhulin, I. B. (2005). One-component systems dominate signal transduction in prokaryotes. Trends in Microbiology, 13(2), 52-56. doi:10.1016/j.tim.2004.12.006

Kiel, C., Yus, E., & Serrano, L. (2010). Engineering Signal Transduction Pathways. Cell, 140(1), 33-47. doi:10.1016/j.cell.2009.12.028

Isaacs, F. J., Dwyer, D. J., & Collins, J. J. (2006). RNA synthetic biology. Nature Biotechnology, 24(5), 545-554. doi:10.1038/nbt1208 [+]
Ulrich, L. E., Koonin, E. V., & Zhulin, I. B. (2005). One-component systems dominate signal transduction in prokaryotes. Trends in Microbiology, 13(2), 52-56. doi:10.1016/j.tim.2004.12.006

Kiel, C., Yus, E., & Serrano, L. (2010). Engineering Signal Transduction Pathways. Cell, 140(1), 33-47. doi:10.1016/j.cell.2009.12.028

Isaacs, F. J., Dwyer, D. J., & Collins, J. J. (2006). RNA synthetic biology. Nature Biotechnology, 24(5), 545-554. doi:10.1038/nbt1208

Liang, J. C., Bloom, R. J., & Smolke, C. D. (2011). Engineering Biological Systems with Synthetic RNA Molecules. Molecular Cell, 43(6), 915-926. doi:10.1016/j.molcel.2011.08.023

Dueber, J. E. (2003). Reprogramming Control of an Allosteric Signaling Switch Through Modular Recombination. Science, 301(5641), 1904-1908. doi:10.1126/science.1085945

Sallee, N. A., Yeh, B. J., & Lim, W. A. (2007). Engineering Modular Protein Interaction Switches by Sequence Overlap. Journal of the American Chemical Society, 129(15), 4606-4611. doi:10.1021/ja0672728

Rodrigo, G., Landrain, T. E., Shen, S., & Jaramillo, A. (2013). A new frontier in synthetic biology: automated design of small RNA devices in bacteria. Trends in Genetics, 29(9), 529-536. doi:10.1016/j.tig.2013.06.005

Callura, J. M., Dwyer, D. J., Isaacs, F. J., Cantor, C. R., & Collins, J. J. (2010). Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proceedings of the National Academy of Sciences, 107(36), 15898-15903. doi:10.1073/pnas.1009747107

Callura, J. M., Cantor, C. R., & Collins, J. J. (2012). Genetic switchboard for synthetic biology applications. Proceedings of the National Academy of Sciences, 109(15), 5850-5855. doi:10.1073/pnas.1203808109

Werstuck, G. (1998). Controlling Gene Expression in Living Cells Through Small Molecule-RNA Interactions. Science, 282(5387), 296-298. doi:10.1126/science.282.5387.296

Wieland, M., & Hartig, J. S. (2008). Improved Aptazyme Design and In Vivo Screening Enable Riboswitching in Bacteria. Angewandte Chemie International Edition, 47(14), 2604-2607. doi:10.1002/anie.200703700

Win, M. N., & Smolke, C. D. (2007). A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proceedings of the National Academy of Sciences, 104(36), 14283-14288. doi:10.1073/pnas.0703961104

Klauser, B., & Hartig, J. S. (2013). An engineered small RNA-mediated genetic switch based on a ribozyme expression platform. Nucleic Acids Research, 41(10), 5542-5552. doi:10.1093/nar/gkt253

Bayer, T. S., & Smolke, C. D. (2005). Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nature Biotechnology, 23(3), 337-343. doi:10.1038/nbt1069

Qi, L., Lucks, J. B., Liu, C. C., Mutalik, V. K., & Arkin, A. P. (2012). Engineering naturally occurring trans -acting non-coding RNAs to sense molecular signals. Nucleic Acids Research, 40(12), 5775-5786. doi:10.1093/nar/gks168

Looger, L. L., Dwyer, M. A., Smith, J. J., & Hellinga, H. W. (2003). Computational design of receptor and sensor proteins with novel functions. Nature, 423(6936), 185-190. doi:10.1038/nature01556

Kortemme, T., & Baker, D. (2004). Computational design of protein–protein interactions. Current Opinion in Chemical Biology, 8(1), 91-97. doi:10.1016/j.cbpa.2003.12.008

Rodrigo, G., Landrain, T. E., & Jaramillo, A. (2012). De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. Proceedings of the National Academy of Sciences, 109(38), 15271-15276. doi:10.1073/pnas.1203831109

Isaacs, F. J., Dwyer, D. J., Ding, C., Pervouchine, D. D., Cantor, C. R., & Collins, J. J. (2004). Engineered riboregulators enable post-transcriptional control of gene expression. Nature Biotechnology, 22(7), 841-847. doi:10.1038/nbt986

Kirkpatrick, S., Gelatt, C. D., & Vecchi, M. P. (1983). Optimization by Simulated Annealing. Science, 220(4598), 671-680. doi:10.1126/science.220.4598.671

Hofacker, I. L., Fontana, W., Stadler, P. F., Bonhoeffer, L. S., Tacker, M., & Schuster, P. (1994). Fast folding and comparison of RNA secondary structures. Monatshefte f�r Chemie Chemical Monthly, 125(2), 167-188. doi:10.1007/bf00818163

Pédelacq, J.-D., Cabantous, S., Tran, T., Terwilliger, T. C., & Waldo, G. S. (2005). Engineering and characterization of a superfolder green fluorescent protein. Nature Biotechnology, 24(1), 79-88. doi:10.1038/nbt1172

Hersch, G. L., Baker, T. A., & Sauer, R. T. (2004). SspB delivery of substrates for ClpXP proteolysis probed by the design of improved degradation tags. Proceedings of the National Academy of Sciences, 101(33), 12136-12141. doi:10.1073/pnas.0404733101

Rodrigo, G., Kirov, B., Shen, S., & Jaramillo, A. (2013). Theoretical and experimental analysis of the forced LacI-AraC oscillator with a minimal gene regulatory model. Chaos: An Interdisciplinary Journal of Nonlinear Science, 23(2), 025109. doi:10.1063/1.4809786

Danino, T., Mondragón-Palomino, O., Tsimring, L., & Hasty, J. (2010). A synchronized quorum of genetic clocks. Nature, 463(7279), 326-330. doi:10.1038/nature08753

Mathews, D. H., Sabina, J., Zuker, M., & Turner, D. H. (1999). Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. Journal of Molecular Biology, 288(5), 911-940. doi:10.1006/jmbi.1999.2700

Paige, J. S., Nguyen-Duc, T., Song, W., & Jaffrey, S. R. (2012). Fluorescence Imaging of Cellular Metabolites with RNA. Science, 335(6073), 1194-1194. doi:10.1126/science.1218298

Chen, X., & Ellington, A. D. (2009). Design Principles for Ligand-Sensing, Conformation-Switching Ribozymes. PLoS Computational Biology, 5(12), e1000620. doi:10.1371/journal.pcbi.1000620

Quarta, G., Sin, K., & Schlick, T. (2012). Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function. PLoS Computational Biology, 8(2), e1002368. doi:10.1371/journal.pcbi.1002368

Freeman, J. B., & Dale, R. (2012). Assessing bimodality to detect the presence of a dual cognitive process. Behavior Research Methods, 45(1), 83-97. doi:10.3758/s13428-012-0225-x

Wieland, M., Benz, A., Klauser, B., & Hartig, J. S. (2009). Artificial Ribozyme Switches Containing Natural Riboswitch Aptamer Domains. Angewandte Chemie International Edition, 48(15), 2715-2718. doi:10.1002/anie.200805311

Penchovsky, R., & Breaker, R. R. (2005). Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nature Biotechnology, 23(11), 1424-1433. doi:10.1038/nbt1155

Chushak, Y., & Stone, M. O. (2009). In silico selection of RNA aptamers. Nucleic Acids Research, 37(12), e87-e87. doi:10.1093/nar/gkp408

Bartel, D., & Szostak, J. (1993). Isolation of new ribozymes from a large pool of random sequences [see comment]. Science, 261(5127), 1411-1418. doi:10.1126/science.7690155

Lutz, R. (1997). Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Research, 25(6), 1203-1210. doi:10.1093/nar/25.6.1203

Mutalik, V. K., Qi, L., Guimaraes, J. C., Lucks, J. B., & Arkin, A. P. (2012). Rationally designed families of orthogonal RNA regulators of translation. Nature Chemical Biology, 8(5), 447-454. doi:10.1038/nchembio.919

Bennett, M. R., & Hasty, J. (2009). Microfluidic devices for measuring gene network dynamics in single cells. Nature Reviews Genetics, 10(9), 628-638. doi:10.1038/nrg2625

Cookson, N. A., Mather, W. H., Danino, T., Mondragón‐Palomino, O., Williams, R. J., Tsimring, L. S., & Hasty, J. (2011). Queueing up for enzymatic processing: correlated signaling through coupled degradation. Molecular Systems Biology, 7(1), 561. doi:10.1038/msb.2011.94

Hermann, T. (2000). Adaptive Recognition by Nucleic Acid Aptamers. Science, 287(5454), 820-825. doi:10.1126/science.287.5454.820

Lou, C., Stanton, B., Chen, Y.-J., Munsky, B., & Voigt, C. A. (2012). Ribozyme-based insulator parts buffer synthetic circuits from genetic context. Nature Biotechnology, 30(11), 1137-1142. doi:10.1038/nbt.2401

Qi, L., Haurwitz, R. E., Shao, W., Doudna, J. A., & Arkin, A. P. (2012). RNA processing enables predictable programming of gene expression. Nature Biotechnology, 30(10), 1002-1006. doi:10.1038/nbt.2355

Liu, C. C., Qi, L., Lucks, J. B., Segall-Shapiro, T. H., Wang, D., Mutalik, V. K., & Arkin, A. P. (2012). An adaptor from translational to transcriptional control enables predictable assembly of complex regulation. Nature Methods, 9(11), 1088-1094. doi:10.1038/nmeth.2184

Qi, L. S., Larson, M. H., Gilbert, L. A., Doudna, J. A., Weissman, J. S., Arkin, A. P., & Lim, W. A. (2013). Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression. Cell, 152(5), 1173-1183. doi:10.1016/j.cell.2013.02.022

Gilbert, L. A., Larson, M. H., Morsut, L., Liu, Z., Brar, G. A., Torres, S. E., … Qi, L. S. (2013). CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes. Cell, 154(2), 442-451. doi:10.1016/j.cell.2013.06.044

Bashor, C. J., Horwitz, A. A., Peisajovich, S. G., & Lim, W. A. (2010). Rewiring Cells: Synthetic Biology as a Tool to Interrogate the Organizational Principles of Living Systems. Annual Review of Biophysics, 39(1), 515-537. doi:10.1146/annurev.biophys.050708.133652

Yen, L., Svendsen, J., Lee, J.-S., Gray, J. T., Magnier, M., Baba, T., … Mulligan, R. C. (2004). Exogenous control of mammalian gene expression through modulation of RNA self-cleavage. Nature, 431(7007), 471-476. doi:10.1038/nature02844

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