scholarly journals Promoter analysis of the Chilo iridescent virus DNA polymerase and major capsid protein genes

Virology ◽  
2003 ◽  
Vol 317 (2) ◽  
pp. 321-329 ◽  
Author(s):  
Remziye Nalçacioğlu ◽  
Hendrik Marks ◽  
Just M. Vlak ◽  
Zihni Demirbaĝ ◽  
Monique M. van Oers
Keyword(s):  
Capsid Protein ◽  
Dna Polymerase ◽  
Promoter Analysis ◽  
Major Capsid Protein ◽  
Chilo Iridescent Virus ◽  
Iridescent Virus

scholarly journals Ranavirus phylogeny and differentiation based on major capsid protein, DNA polymerase and neurofilament triplet H1-like protein genes

2009 ◽  
Vol 85 ◽  
pp. 81-91 ◽  
Author(s):  
R Holopainen ◽  
S Ohlemeyer ◽  
H Schütze ◽  
SM Bergmann ◽  
H Tapiovaara
Keyword(s):  
Capsid Protein ◽  
Dna Polymerase ◽  
Major Capsid Protein

scholarly journals Medusavirus, a Novel Large DNA Virus Discovered from Hot Spring Water

2019 ◽  
Vol 93 (8) ◽  
Author(s):  
Genki Yoshikawa ◽  
Romain Blanc-Mathieu ◽  
Chihong Song ◽  
Yoko Kayama ◽  
Tomohiro Mochizuki ◽  
...  
Keyword(s):  
Dna Replication ◽  
Capsid Protein ◽  
Dna Polymerase ◽  
Major Capsid Protein ◽  
Hot Spring ◽  
Morphological Characteristics ◽  
Spring Water ◽  
Dna Virus ◽  
Dna Viruses ◽  
Content Type

ABSTRACT Recent discoveries of new large DNA viruses reveal high diversity in their morphologies, genetic repertoires, and replication strategies. Here, we report the novel features of medusavirus, a large DNA virus newly isolated from hot spring water in Japan. Medusavirus, with a diameter of 260 nm, shows a T=277 icosahedral capsid with unique spherical-headed spikes on its surface. It has a 381-kb genome encoding 461 putative proteins, 86 of which have their closest homologs in Acanthamoeba, whereas 279 (61%) are orphan genes. The virus lacks the genes encoding DNA topoisomerase II and RNA polymerase, showing that DNA replication takes place in the host nucleus, whereas the progeny virions are assembled in the cytoplasm. Furthermore, the medusavirus genome harbored genes for all five types of histones (H1, H2A, H2B, H3, and H4) and one DNA polymerase, which are phylogenetically placed at the root of the eukaryotic clades. In contrast, the host amoeba encoded many medusavirus homologs, including the major capsid protein. These facts strongly suggested that amoebae are indeed the most promising natural hosts of medusavirus, and that lateral gene transfers have taken place repeatedly and bidirectionally between the virus and its host since the early stage of their coevolution. Medusavirus reflects the traces of direct evolutionary interactions between the virus and eukaryotic hosts, which may be caused by sharing the DNA replication compartment and by evolutionarily long lasting virus-host relationships. Based on its unique morphological characteristics and phylogenomic relationships with other known large DNA viruses, we propose that medusavirus represents a new family, Medusaviridae. IMPORTANCE We have isolated a new nucleocytoplasmic large DNA virus (NCLDV) from hot spring water in Japan, named medusavirus. This new NCLDV is phylogenetically placed at the root of the eukaryotic clades based on the phylogenies of several key genes, including that encoding DNA polymerase, and its genome surprisingly encodes the full set of histone homologs. Furthermore, its laboratory host, Acanthamoeba castellanii, encodes many medusavirus homologs in its genome, including the major capsid protein, suggesting that the amoeba is the genuine natural host from ancient times of this newly described virus and that lateral gene transfers have repeatedly occurred between the virus and amoeba. These results suggest that medusavirus is a unique NCLDV preserving ancient footprints of evolutionary interactions with its hosts, thus providing clues to elucidate the evolution of NCLDVs, eukaryotes, and virus-host interaction. Based on the dissimilarities with other known NCLDVs, we propose that medusavirus represents a new viral family, Medusaviridae.

scholarly journals The Chilo iridescent virus DNA polymerase promoter contains an essential AAAAT motif

2007 ◽  
Vol 88 (9) ◽  
pp. 2488-2494 ◽  
Author(s):  
Remziye Nalçacioğlu ◽  
Ikbal Agah Ince ◽  
Just M. Vlak ◽  
Zihni Demirbağ ◽  
Monique M. van Oers
Keyword(s):  
Dna Polymerase ◽  
Transcription Initiation ◽  
Promoter Activity ◽  
Transcriptional Start Site ◽  
Point Mutations ◽  
Luciferase Reporter ◽  
Start Site ◽  
Chilo Iridescent Virus ◽  
Luciferase Reporter Gene ◽  
Iridescent Virus

The delayed-early DNA polymerase promoter of Chilo iridescent virus (CIV), officially known as Invertebrate iridescent virus, was fine mapped by constructing a series of increasing deletions and by introducing point mutations. The effects of these mutations were examined in a luciferase reporter gene system using Bombyx mori cells transfected with promoter constructs and infected with CIV. When the size of the upstream element was reduced from position −19 to −15, relative to the transcriptional start site, the luciferase activity was reduced to almost zero. Point mutations showed that each of the 5 nt (AAAAT) located between –19 and –15 were equally essential for promoter activity. Mutations at individual bases around the transcription initiation site showed that the promoter extended until position −2 upstream of the transcription start site. South-Western analysis showed that a protein of approximately 100 kDa interacted with the −19 nt promoter fragment in CIV-infected cells. This binding did not occur with a point mutant that lacked promoter activity. The AAAAT motif was also found in the DNA polymerase promoter region of other iridoviruses and in other putative CIV delayed-early genes.

scholarly journals Unveiling of the Diversity of Prasinoviruses (Phycodnaviridae) in Marine Samples by Using High-Throughput Sequencing Analyses of PCR-Amplified DNA Polymerase and Major Capsid Protein Genes

2014 ◽  
Vol 80 (10) ◽  
pp. 3150-3160 ◽  
Author(s):  
Camille Clerissi ◽  
Nigel Grimsley ◽  
Hiroyuki Ogata ◽  
Pascal Hingamp ◽  
Julie Poulain ◽  
...  
Keyword(s):  
Capsid Protein ◽  
Dna Polymerase ◽  
High Throughput Sequencing ◽  
Major Capsid Protein ◽  
Content Type ◽  
Chain Reactions ◽  
Polymerase Chain Reactions ◽  
Genes Encoding ◽  
Conserved Genes ◽  
Primer Sets

ABSTRACTViruses strongly influence the ecology and evolution of their eukaryotic hosts in the marine environment, but little is known about their diversity and distribution. Prasinoviruses infect an abundant and widespread class of phytoplankton, the Mamiellophyceae, and thereby exert a specific and important role in microbial ecosystems. However, molecular tools to specifically identify this viral genus in environmental samples are still lacking. We developed two primer sets, designed for use with polymerase chain reactions and 454 pyrosequencing technologies, to target two conserved genes, encoding the DNA polymerase (PolB gene) and the major capsid protein (MCP gene). While only one copy of the PolB gene is present inPrasinovirusgenomes, there are at least seven paralogs for MCP, the copy we named number 6 being shared with other eukaryotic alga-infecting viruses. Primer sets for PolB and MCP6 were thus designed and tested on 6 samples from the Tara Oceans project. The results suggest that the MCP6 amplicons show greater richness but that PolB gave a wider coverage ofPrasinovirusdiversity. As a consequence, we recommend use of the PolB primer set, which will certainly reveal exciting new insights about the diversity and distribution of prasinoviruses at the community scale.

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