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Cervera H, Ambrós S, Bernet GP, Rodrigo G, Elena SF. Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host's Transcriptome: The Tobacco Etch Potyvirus-Tobacco Case Study. Mol Biol Evol 2018; 35:1599-1615. [PMID: 29562354 PMCID: PMC5995217 DOI: 10.1093/molbev/msy038] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Determining the fitness of viral genotypes has become a standard practice in virology as it is essential to evaluate their evolutionary potential. Darwinian fitness, defined as the advantage of a given genotype with respect to a reference one, is a complex property that captures, in a single figure, differences in performance at every stage of viral infection. To what extent does viral fitness result from specific molecular interactions with host factors and regulatory networks during infection? Can we identify host genes in functional classes whose expression depends on viral fitness? Here, we compared the transcriptomes of tobacco plants infected with seven genotypes of tobacco etch potyvirus that differ in fitness. We found that the larger the fitness differences among genotypes, the more dissimilar the transcriptomic profiles are. Consistently, two different mutations, one in the viral RNA polymerase and another in the viral suppressor of RNA silencing, resulted in significantly similar gene expression profiles. Moreover, we identified host genes whose expression showed a significant correlation, positive or negative, with the virus' fitness. Differentially expressed genes which were positively correlated with viral fitness activate hormone- and RNA silencing-mediated pathways of plant defense. In contrast, those that were negatively correlated with fitness affect metabolism, reducing growth, and development. Overall, these results reveal the high information content of viral fitness and suggest its potential use to predict differences in genomic profiles of infected hosts.
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Affiliation(s)
- Héctor Cervera
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnia de València, Campus UPV CPI 8E, València, Spain
| | - Silvia Ambrós
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnia de València, Campus UPV CPI 8E, València, Spain
| | - Guillermo P Bernet
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnia de València, Campus UPV CPI 8E, València, Spain
| | - Guillermo Rodrigo
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnia de València, Campus UPV CPI 8E, València, Spain
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, Parc Científic UV, Catedrático Agustín Escardino 9, Paterna, València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnia de València, Campus UPV CPI 8E, València, Spain
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, Parc Científic UV, Catedrático Agustín Escardino 9, Paterna, València, Spain
- The Santa Fe Institute, Santa Fe, NM
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Eschenfeldt WH, Maltseva N, Stols L, Donnelly MI, Gu M, Nocek B, Tan K, Kim Y, Joachimiak A. Cleavable C-terminal His-tag vectors for structure determination. J Struct Funct Genomics 2010; 11:31-9. [PMID: 20213425 PMCID: PMC2885959 DOI: 10.1007/s10969-010-9082-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Accepted: 02/11/2010] [Indexed: 10/19/2022]
Abstract
High-throughput structural genomics projects seek to delineate protein structure space by determining the structure of representatives of all major protein families. Generally this is accomplished by processing numerous proteins through standardized protocols, for the most part involving purification of N-terminally His-tagged proteins. Often proteins that fail this approach are abandoned, but in many cases further effort is warranted because of a protein's intrinsic value. In addition, failure often occurs relatively far into the path to structure determination, and many failed proteins passed the first critical step, expression as a soluble protein. Salvage pathways seek to recoup the investment in this subset of failed proteins through alternative cloning, nested truncations, chemical modification, mutagenesis, screening buffers, ligands and modifying processing steps. To this end we have developed a series of ligation-independent cloning expression vectors that append various cleavable C-terminal tags instead of the conventional N-terminal tags. In an initial set of 16 proteins that failed with an N-terminal appendage, structures were obtained for C-terminally tagged derivatives of five proteins, including an example for which several alternative salvaging steps had failed. The new vectors allow appending C-terminal His(6)-tag and His(6)- and MBP-tags, and are cleavable with TEV or with both TEV and TVMV proteases.
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Affiliation(s)
- William H. Eschenfeldt
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Bldg. 202/Rm. BE111, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Natalia Maltseva
- Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, IL 60667, USA
| | - Lucy Stols
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Bldg. 202/Rm. BE111, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Mark I. Donnelly
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Bldg. 202/Rm. BE111, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Minyi Gu
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Bldg. 202/Rm. BE111, 9700 South Cass Avenue, Argonne, IL 60439, USA; Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, IL 60667, USA
| | - Boguslaw Nocek
- Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, IL 60667, USA
| | - Kemin Tan
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Bldg. 202/Rm. BE111, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Youngchang Kim
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Bldg. 202/Rm. BE111, 9700 South Cass Avenue, Argonne, IL 60439, USA; Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, IL 60667, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Bldg. 202/Rm. BE111, 9700 South Cass Avenue, Argonne, IL 60439, USA; Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, IL 60667, USA
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