Graduate Thesis Or Dissertation
 

Fine structure of the virus genome in a marine filamentous brown algae, Feldmannia

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  • Viruses or viruslike particles of eukaryotic algae are ubiquitous in aquatic habitats, however, suprisingly little is known about them. The research presented here focused on one such virus which infects a multicellular filamentous brown alga of the genus Feldmannia. Although preliminary studies had been performed on the genome structure of the Feldmannia sp. Virus (FsV), little was known. The purpose of this study was to analyze the structure of the FsV genome in detail. During the experiments aimed at mapping the FsV genome, cross-hybridization was observed among five BamHI-fragments of the digested FsV DNA. Sequence analysis of one of those fragments revealed the presence of 173 by direct repeats. There are two FsV genomes of different size-classes (158 and 178 kbp). The 173 by repeats in the cross-hybridizing BamHI-fragments were confined to a small region of each virus genome. The number of these repeats in the 178 kbp genome was estimated to be about 109 and in the 158 kbp genome to be about 41. in the 178 kbp genome, the repeats are contained within a 22 kbp region and in the 1.58 kbp genome, the repeats are contained within a 10 kbp region. These viruses are actively replicated in sporophyte plants. A family of related 173 by direct repeats was discovered in an encrypted FsV genome. The family of repeats estimated to be greater than 50 kbp in length were found inserted into a protein kinase gene encoded within the 3.6 kbp viral BamHI-fragment Z. Southern analysis indicates that these repeats in the encrypted FsV genome are distinct from the previously characterized repeats in the amplified FsV genome. The translated protein kinase shares highest homologies to the SNF1 subfamily of serine/threonine protein kinases and contains a potential autophosphorylation site in a region unique to this protein kinase. A DNA polymerase gene was identified in the FsV genome. The predicted peptide sequence of the FsV DNA polymerase gene contains all of the conserved motifs found in B-family (a-like) DNA polymerases. A TTTTTNT sequence motif shown to be a transcription termination signal for Vaccinia virus early genes is found at the 3' end of the DNA polymerase gene. Phylogenetic analysis of the FsV DNA polymerase gene and other viral DNA polymerase genes indicates that FsV belongs to a group of algal viruses recently defined as Phycodnaviridae.
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