The modulation of Nicotiana benthamiana gene expression by Red clover necrotic mosaic virus

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Title: The modulation of Nicotiana benthamiana gene expression by Red clover necrotic mosaic virus
Author: Feulner, Gretchen Elizabeth
Advisors: Steven A. Lommel, Committee Chair
Abstract: Nicotiana benthamiana, a member of the Solanaceae family, is an amphidiploid species with n=19 chromosomes. It is the premier host for the maintenance and study of plant virus/host interactions. Not only is it susceptible to a large number of monocot and dicot infecting RNA plant viruses, but it has also been shown to serve as a host for an RNA insect virus. In collaboration with NimbleGen Systems, Inc (Madison, WI), we developed and validated a microarray from N. benthamiana expressed sequence tags (ESTs). The array is composed of oligonucleotides (60mers) corresponding to 13,014 N. benthamiana ESTs, equivalent to an estimated coverage of approximately 38% of the N. benthamiana transcriptome. The majority of previous studies that have investigated global plant host gene expression changes during a viral infection have used the Affymetrix Arabidopsis thaliana gene chip. Additionally, only one of these studies has considered changes that occur within the first 24 hours after inoculation. We are interested in the changes that occur in N. benthamiana early in the infection process by an RNA plant virus. Our goal was to study these early changes by challenging N. benthamiana with Red clover necrotic mosaic virus (RCNMV). RCNMV, a member of the Dianthovirus genus, is a bipartite, single stranded, positive sense RNA virus. Total RNA, from mock and RCNMV infected N. benthamiana was isolated from leaves at 2, 6, 12 and 24 hours post inoculation (hpi) and hybridized to the N. benthamiana microarrays. Statistical analysis determined a total of 1,775 ESTs exhibited differential expression for at least one timepoint in response to infection by RCNMV. As determined in other array experiments employing plant viruses, the preponderance of these genes are related to those known or predicted to be involved in pathogen defense. Key host pathways affected by the infection, as determined by Gene Ontology functional classifications, include metabolism, transport, membrane/cell wall associated, and defense-related genes. We hypothesize that the observed suppression and induction of these genes relates directly to the host factors required by the virus at each stage of its life cycle. This is the first report of a N. benthamiana microarray used to monitor host gene expression profiles upon virus infection at a sub 24 hpi timeframe.
Date: 2008-11-09
Degree: MS
Discipline: Genetics

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