Chlorella virus
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ABSTRACT:
PROVIDER: PRJNA342147 | ENA |
REPOSITORIES: ENA
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Project description:Paramecium bursaria chlorella virus (PBCV-1), a member of the family Phycodnaviridae, is a large dsDNA, plaque-forming virus that infects the unicellular green alga Chlorella NC64A. The 331 kb PBCV-1 genome is predicted to encode 365 proteins and 11 tRNAs. To follow global transcription during PBCV-1 replication, a microarray containing 50-mer probes to the PBCV-1 365 protein-encoding genes (CDS) was constructed. Competitive hybridization experiments were conducted employing cDNA from poly A-containing RNA obtained from cells at seven time points after virus infection. The results led to the following conclusions: i) the PBCV-1 replication cycle is temporally programmed and regulated; ii) 360 (99%) of the arrayed PBCV-1 CDSs are expressed at some time in the virus life cycle in the laboratory; iii) 227 (62%) of the CDSs are expressed before virus DNA synthesis begins; iv) these 227 CDSs were grouped into two classes: 127 transcripts disappear prior to initiation of virus DNA synthesis (considered early) and 100 transcripts are still detected after virus DNA synthesis begins (considered early/late); v) 133 (36%) of the CDSs are expressed after virus DNA synthesis begins (considered late); vi) expression of most late CDSs is inhibited by adding the DNA replication inhibitor aphidicolin prior to virus infection. This study provides the first comprehensive evaluation of virus gene expression during the PBCV-1 lifecycle.
2010-01-10 | GSE18421 | GEO
Project description:Paramecium bursaria chlorella virus (PBCV-1), a member of the family Phycodnaviridae, is a large dsDNA, plaque-forming virus that infects the unicellular green alga Chlorella NC64A. The 331 kb PBCV-1 genome is predicted to encode 365 proteins and 11 tRNAs. To follow global transcription during PBCV-1 replication, a microarray containing 50-mer probes to the PBCV-1 365 protein-encoding genes (CDS) was constructed. Competitive hybridization experiments were conducted employing cDNA from poly A-containing RNA obtained from cells at seven time points after virus infection. The results led to the following conclusions: i) the PBCV-1 replication cycle is temporally programmed and regulated; ii) 360 (99%) of the arrayed PBCV-1 CDSs are expressed at some time in the virus life cycle in the laboratory; iii) 227 (62%) of the CDSs are expressed before virus DNA synthesis begins; iv) these 227 CDSs were grouped into two classes: 127 transcripts disappear prior to initiation of virus DNA synthesis (considered early) and 100 transcripts are still detected after virus DNA synthesis begins (considered early/late); v) 133 (36%) of the CDSs are expressed after virus DNA synthesis begins (considered late); vi) expression of most late CDSs is inhibited by adding the DNA replication inhibitor aphidicolin prior to virus infection. This study provides the first comprehensive evaluation of virus gene expression during the PBCV-1 lifecycle. Time course analysis of chlorella virus PBCV-1: cDNAs from poly A-containing RNAs isolated from cells at seven times after PBCV-1 infection (20, 40, 60, 90, 120, 240, 360 min p.i.) were competitively hybridized against a reference sample on the microarrays. Three independent biological replica, four technical replica of the genome per array. Time course analysis of chlorella virus PBCV-1 gene expression in the presence of aphidicolin: cDNAs from poly A-containing RNAs isolated from aphidicolin-treated cells at seven times after PBCV-1 infection (20, 40, 60, 90, 120, 240, 360 min p.i.) were competitively hybridized against non-treated, infected samples from the same time points. Three independent biological replica, four technical replica of the genome per array.
2010-05-16 | E-GEOD-18421 | biostudies-arrayexpress
Project description:Microarray analysis of Chlorella Virus PBCV-1 Transcription during the viral lifecycle
| PRJNA118217 | ENA
Project description:SMRT sequencing of Paramecium bursaria Chlorella Virus-1 reveals dynamic methylation patterns in adenines targeted by RM-systems
| PRJNA544680 | ENA
Project description:Small RNA libraries were constructed from total RNA from Jasminum sambac plants exhibiting virus-like symptoms. After sequencing, small RNAs were assembled into contigs with MetaVelvet and assembled contigs were aligned against the NR database of NCBI using BLASTx. Top hits that reported a virus as subject were considered putative viral sequences. Based on such alignments, the whole genome of a virus, we tentatively name Jasmine Virus H was recovered and cloned. Two more small RNA libraries were made in a confirmatory experiment. One from Jasminum sambac and another one from Nicotiana benthamiana plants infected with the newly-cloned virus. The small RNA libraries were aligned against the full-length sequence of Jasmine Virus H to determine the spacial distribution of virus-derived small RNAs along the virus genome.
2018-01-01 | GSE96704 | GEO
Project description:We report the genetic plasticity of Sendai virus and mumps virus. We introduced insertional mutation in the virus genome and checked fitness by comparing distribution of mutans in passage 1 and passage 2.
2019-02-01 | GSE125257 | GEO
Project description:We report the application of high throughput sequencing technology for investigating the transcriptional regulatory network of the human innate immune response. With ChIP-seq, we generated genome-wide virus-activated transcription factor and transcription machinery maps of infected and uninfected human Namalwa B cells. Analysis of ChIP-seq data reveals extensive collaboration of IRF3 and NF-κB with Mediator throughout the human genome, and implicates additional transcription factor partners in antiviral responses. Moreover, analysis of Pol II occupancy and elongation status during virus infection indicates that IRF3 and NF-κB drive both de novo polymerase recruitment and mediate polymerase pause-release at their target sites, stimulating the expression of a variety of protein-coding, non-coding, and unannotated loci. Examination of 6 different proteins before and after virus infection in 1 cell type.
2013-08-28 | E-GEOD-44939 | biostudies-arrayexpress
Project description:Grapevine line pattern virus (GLPV) was described 30 years ago from Hungary, and in the lack of its sequence until now no additional information about its presence was reported. However High-Throughput Sequencing (HTS) applied on dsRNAs extracts recovered from a grapevine plant (accession Baco22A) infected with GLPV Grapevine line pattern virus (GLPV) allowed us to sequence it with different High-Throughput Sequencing (HTS) methods andthe assembleing of the full genome sequence of this virus. The availability of the sequence allowed us to validate the presence of the virus bot with RT-PCR and with Northern blot hybridization. These methods were also used to test its graft and seed transmission. In accordance as it was originally suggested its genome was found to comprise three RNA segments.Its RNA1 (3.160 bp), RNA2 (2.493 bp) and RNA3 (2.529 bp), encode four proteins, denoted 1a (Methyltransferase, helicase), 2a (RNA-dependent RNA Polymerase), 3a (Movement protein, MP) and 3b (Coat protein, CP). GLPV showed the highest amino acid identity (92%–99%) with all domains of Hop yellow virus (HYV), which is a tentative member of the genus Anulavirus of the family Bromoviridae. The phylogenetic trees constructed based on the amino acid sequences of 2a and 3b also confirmed the belongingness of GLPV to the genus Anulavirus, allocating it in one cluster together with the anulaviruses, and close to HYV. The very high sequence identity found between GLPV and HYV leaves no doubt that both are two isolates of the same viral species.
2020-06-03 | GSE148246 | GEO
Project description:To search for host factors regulating Zika virus infection, we performed a genome-wide loss-of-function CRISPR/Cas9 screen in haploid human ESCs. The regulators were identified by the quantification of enrichment of their mutant clones within a pooled loss-of-function library upon Zika virus infection.
2023-05-31 | E-MTAB-11945 | biostudies-arrayexpress