- -

Computational design of host transcription-factors sets whose misregulation mimics the transcriptomic effect of viral infections

RiuNet: Repositorio Institucional de la Universidad Politécnica de Valencia

Compartir/Enviar a

Citas

Estadísticas

  • Estadisticas de Uso

Computational design of host transcription-factors sets whose misregulation mimics the transcriptomic effect of viral infections

Mostrar el registro completo del ítem

Carrera Montesinos, J.; Elena Fito, SF. (2012). Computational design of host transcription-factors sets whose misregulation mimics the transcriptomic effect of viral infections. Scientific Reports. 2:1-10. https://doi.org/10.1038/srep01006

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/81387

Ficheros en el ítem

Metadatos del ítem

Título: Computational design of host transcription-factors sets whose misregulation mimics the transcriptomic effect of viral infections
Autor: Carrera Montesinos, Javier Elena Fito, Santiago Fco
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
Universitat Politècnica de València. Instituto de Instrumentación para Imagen Molecular - Institut d'Instrumentació per a Imatge Molecular
Fecha difusión:
Resumen:
[EN] The molecular mechanisms underlying viral pathogenesis are yet poorly understood owed to the large number of factors involved and the complexity of their interactions. Could we identify a minimal set of host transcription ...[+]
Palabras clave: GENE-EXPRESSION PROFILE , ARABIDOPSIS-THALIANA , VIRUS-INFECTION , MOSAIC-VIRUS , GEMINIVIRUS INFECTION , PATHOGEN INTERACTIONS , ADENOSINE KINASE , SYSTEMS BIOLOGY , L2 PROTEINS , NETWORKS
Derechos de uso: Reserva de todos los derechos
Fuente:
Scientific Reports. (issn: 2045-2322 )
DOI: 10.1038/srep01006
Editorial:
Nature Publishing Group
Versión del editor: http://doi.org/10.1038/srep01006
Código del Proyecto:
info:eu-repo/grantAgreement/MICINN//BFU2009-06993/ES/Biologia Evolutiva Y De Sistemas De La Emergencia De Fitovirus De Rna/
Agradecimientos:
We thank J.A. Daros, M. A. Fares and G. Rodrigo for fruitful comments and suggestions and O. Voinnet and C. Llave for sharing with us the TCV and TRV transcriptomic data, respectively. This research was supported by grant ...[+]
Tipo: Artículo

References

Dodds, P. N. & Rathjen, J. P. Plant immunity: towards an integrated view of plant-pathogen interactions. Nat Rev Genet 11, 539–48 (2010).

Jenner, R. G. & Young, R. A. Insights into host responses against pathoghens from transcriptional profiling. Nat Rev Microbiol 3, 281–94 (2005).

Andeweg, A. C., Haagmans, B. L. & Osterhaus, A. D. Virogenomics: the virus-host interaction revisited. Curr Opin Microbiol 11, 461–6 (2008). [+]
Dodds, P. N. & Rathjen, J. P. Plant immunity: towards an integrated view of plant-pathogen interactions. Nat Rev Genet 11, 539–48 (2010).

Jenner, R. G. & Young, R. A. Insights into host responses against pathoghens from transcriptional profiling. Nat Rev Microbiol 3, 281–94 (2005).

Andeweg, A. C., Haagmans, B. L. & Osterhaus, A. D. Virogenomics: the virus-host interaction revisited. Curr Opin Microbiol 11, 461–6 (2008).

Elena, S. F., Carrera, J. & Rodrigo, G. A systems biology approach to the evolution of plant-virus interactions. Curr Opin Plant Biol 14, 372–7 (2011).

Friedel, C. C. & Haas, J. Virus-host interactomes and global models of virus-infected cells. Trends Microbiol 19, 501–8 (2011).

Peng, X. et al. Virus-host interactions: from systems biology to translational research. Curr Opin Microbiol 12, 432–8 (2009).

Tan, S. L., Ganji, G., Paeper, B., Proll, S. & Katze, M. G. Systems biology and the host response to viral infection. Nat Biotech 25, 1383–9 (2007).

Wise, R. P., Moscou, M. J., Bogdanove, A. J. & Whitham, S. A. Transcript profiling in host-pathogen interactions. Annu Rev Phytopathol 43, 329–69 (2007).

Agudelo-Romero, P. et al. Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus. Virol J 5, 92 (2008).

Agudelo-Romero, P., Carbonell, P., Pérez-Amador, M. A. & Elena, S. F. Virus adaptation by manipulation of host's gene expression. PLoS ONE 3, e2397 (2008).

Ascencio-Ibáñez, J. et al. Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection. Plant Physiol 148, 436–54 (2008).

Babu, M., Griffiths, J. S., Huang, T. S. & Wang, A. Altered gene expression changes in Arabidopsis leaf tissues and protoplasts in response to Plum pox virus infection. BMC Genomics 9, 325 (2008).

Espinoza, C., Medina, C., Somerville, S. & Arce-Jonhson, P. Senescence-associated genes induced during compatible viral interactions with grapevine and Arabidopsis. J Exp Bot 58, 3197–212 (2007).

Golem, S. & Culver, J. N. Tobacco mosaic virus induced alterations in the gene expression profile of Arabidopsis thaliana. Mol Plant-Microb Interact 16, 681–8 (2003).

Ishihara, T. et al. Comparative analysis of expressed sequence tags in resistant and susceptible ecotypes of Arabidopsis thaliana infected with Cucumber mosaic virus. Plant Cell Physiol 45, 470–80 (2004).

Yang, C. et al. Spatial analysis of Arabidopsis thaliana gene expression in response to Turnip mosaic virus infection. Mol Plant-Microb Interact 20, 358–70 (2007).

Whitham, S. A., Yang, C. & Goodin, M. M. Global impact: elucidating plant responses to viral infection. Mol Plant-Microb Interact 11, 1207–15 (2006).

Whitham, S. A. & Wang, Y. Roles for host factors in plant viral pathogenicity. Curr Opin Plant Biol 7, 365–71 (2004).

Rodrigo, G. et al. A meta-analysis reveals the commonalities and differences in Arabidopsis thaliana response to different viral pathogens. PLoS ONE 7, e40526 (2012).

Bushman, F. D. et al. Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog 5, e1000437 (2009).

Calderwood, M. A. et al. Epstein-Barr virus and virus human protein interaction maps. Proc Natl Acad Sci USA 104, 7606–11 (2007).

De Chassey, B. et al. Hepatitis C virus infection protein network. Mol Syst Biol 4, 230 (2008).

MacPherson, J. I., Dickerson, J. E., Pinney, J. W. & Robertson, D. L. Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems. PLoS Comput Biol 6, e1000863 (2010).

Uetz, P. et al. Herpesviral protein networks and their interaction with the human proteome. Science 311, 239–42 (2006).

Watanabe, T., Watanabe, S. & Kawaoka, Y. Cellular networks involved in the influenza virus life cycle. Cell Host Microbe 7, 427–39 (2010).

Wuchty, S., Siwo, G. & Ferdig, M. T. Viral organization of human proteins. PLoS ONE 5, e11796 (2010).

Di Bernardo, D. et al. Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat Biotech 23, 377–83 (2005).

Carrera, J., Rodrigo, G., Jaramillo, A. & Elena, S. F. Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions. Genome Biol 10, R96 (2009).

Carrera, J., Elena, S. F. & Jaramillo, A. Computational design of genomic transcriptional networks with adaptation to varying environments. Proc Natl Acad Sci USA 109, 15277–82 (2012).

Segrè, D., Vitkup, D. & Church, G. M. Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA 99, 15112–7 (2002).

Burgard, A. P., Pharkya, P. & Maranas, C. D. OptKnock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 84, 647–57 (2003).

Isalan, M. et al. Evolvability and hierarchy in rewired bacterial gene networks. Nature 452, 840–5 (2008).

Kitney, R. & Freemont, P. Synthetic biology – the state of play. FEBS Lett 586, 2029–36 (2012).

Rodrigo, R., Carrera, J., Landrain, T. E. & Jaramillo, A. Perspectives on the automatic design of regulatory systems for synthetic biology. FEBS Lett 586, 2037–42 (2012).

Carrera, J. et al. Fine-tuning tomato agronomic properties by computational genome redesign. PLoS Comput Biol 8, e1002528 (2012).

Carrera, J., Rodrigo, G. & Jaramillo, A. Towards the automated engineering of a synthetic genome. Mol Biosyst 5, 733–43 (2009).

Wang, H., Hao, L., Shung, C. Y., Sunter, G. & Bisaro, D. M. Adenosine kinase is inactivated by geminivirus AL2 and L2 proteins. Plant Cell 15, 3020–32 (2003).

Wang, H., Buckley, K. J., Yang, X., Buchmann, R. C. & Bisaro, D. M. Adenosine kinase inhibition and suppression of RNA silencing by geminivirus AL2 and L2 proteins. J Virol 79, 7410–8 (2005).

Baliji, S., Lacatus, G. & Sunter, G. The interaction between pathogenicity proteins and adenosine kinase leads to increased expression of primary cytokinin-responsive genes. Virology 402, 238–47 (2010).

Shen, W. & Hanley-Bowdoin, L. Geminivirus infection up-regulates the expression of two Arabidopsis protein kinases related to yeast SNF1- and mammalian AMPK-activating kinases. Plant Physiol 142, 1642–55 (2006).

Piroux, N., Saunders, K., Page, A. & Stanley, J. Geminivirus pathogenicity protein C4 interacts with Arabidopsis thaliana shaggy-related protein kinase AtSKeta, a component of the brassinosteroid signaling pathway. Virology 362, 428–40 (2007).

Vogel, J. T., Zarka, D. G., Van Buskirk, H. A., Fowler, S. G. & Thomashow, M. F. Roles of the CBF2 and ZAT12 transcription factors in configuring the low temperature transcriptome of Arabidopsis. Plant J 41, 195–211 (2005).

Lee, C. M. & Thomashow, M. F. Photoperiodic regulation of the C-repeat binding factor (CBF) cold acclimation pathway and freezing tolerance in Arabidopsis thaliana. Proc Natl Acad Sci USA 109, 1504–9 (2012).

Hsieh, T. F. et al. Regulation of imprinted gene expression in Arabidopsis endosperm. Proc Natl Acad Sci USA 108, 1755–62 (2011).

Hirai, M. Y. et al. Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis. Proc Natl Acad Sci USA 104, 6478–83 (2007).

Sønderby, I. E., Burow, M., Rowe, H. C., Kliebenstein, D. J. & Halkier, B. A. A complex interplay of three R2R3 MYB transcription factors determines the profile of aliphatic glucosinolates in Arabidopsis. Plant Physiol 153, 348–63 (2010).

Sønderby, I. E., Geu-Flores, F. & Halkier, B. A. Biosynthesis of glucosinolates – gene discovery and beyond. Trends Plant Sci 15, 283–90 (2010).

Burow, M., Halkier, B. A. & Kliebenstein, D. J. Regulatory networks of glucosinolates shape Arabidopsis thaliana fitness. Curr Opin Plant Biol 13, 347–52 (2010).

[-]

recommendations

 

Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro completo del ítem