Microarray analysis of Paramecium bursaria chlorella virus 1 transcription

Giane M. Yanai-Balser, Garry A. Duncan, James D Eudy, Dong Wang, Xiao Li, Irina V Agarkova, David D Dunigan, James L Van Etten

Research output: Contribution to journalArticle

30 Citations (Scopus)

Abstract

Paramecium bursaria chlorella virus 1 (PBCV-1), a member of the family Phycodnaviridae, is a large double-stranded DNA, plaque-forming virus that infects the unicellular green alga Chlorella sp. strain NC64A. The 330-kb PBCV-1 genome is predicted to encode 365 proteins and 11 tRNAs. To monitor global transcription during PBCV-1 replication, a microarray containing 50-mer probes to the PBCV-1 365 protein-encoding genes (CDSs) was constructed. Competitive hybridization experiments were conducted by using cDNAs from poly(A)-containing RNAs 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 were expressed at some time in the virus life cycle in the laboratory; (iii) 227 (62%) of the CDSs were expressed before virus DNA synthesis begins; (iv) these 227 CDSs were grouped into two classes: 127 transcripts disappeared prior to initiation of virus DNA synthesis (considered early), and 100 transcripts were still detected after virus DNA synthesis begins (considered early/late); (v) 133 (36%) of the CDSs were expressed after virus DNA synthesis begins (considered late); and (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 life cycle.

Original languageEnglish (US)
Pages (from-to)532-542
Number of pages11
JournalJournal of virology
Volume84
Issue number1
DOIs
StatePublished - Jan 1 2010

Fingerprint

Paramecium bursaria Chlorella virus 1
Paramecium
Chlorella
Microarray Analysis
transcription (genetics)
DNA viruses
Viruses
DNA Viruses
viruses
synthesis
Virus Diseases
Virus Replication
Life Cycle Stages
Phycodnaviridae
life cycle (organisms)
Aphidicolin
DNA replication
Chlorophyta
infection
Transfer RNA

ASJC Scopus subject areas

  • Microbiology
  • Immunology
  • Insect Science
  • Virology

Cite this

Microarray analysis of Paramecium bursaria chlorella virus 1 transcription. / Yanai-Balser, Giane M.; Duncan, Garry A.; Eudy, James D; Wang, Dong; Li, Xiao; Agarkova, Irina V; Dunigan, David D; Van Etten, James L.

In: Journal of virology, Vol. 84, No. 1, 01.01.2010, p. 532-542.

Research output: Contribution to journalArticle

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abstract = "Paramecium bursaria chlorella virus 1 (PBCV-1), a member of the family Phycodnaviridae, is a large double-stranded DNA, plaque-forming virus that infects the unicellular green alga Chlorella sp. strain NC64A. The 330-kb PBCV-1 genome is predicted to encode 365 proteins and 11 tRNAs. To monitor global transcription during PBCV-1 replication, a microarray containing 50-mer probes to the PBCV-1 365 protein-encoding genes (CDSs) was constructed. Competitive hybridization experiments were conducted by using cDNAs from poly(A)-containing RNAs 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 were expressed at some time in the virus life cycle in the laboratory; (iii) 227 (62{\%}) of the CDSs were expressed before virus DNA synthesis begins; (iv) these 227 CDSs were grouped into two classes: 127 transcripts disappeared prior to initiation of virus DNA synthesis (considered early), and 100 transcripts were still detected after virus DNA synthesis begins (considered early/late); (v) 133 (36{\%}) of the CDSs were expressed after virus DNA synthesis begins (considered late); and (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 life cycle.",
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