mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus
- Matthieu Legendre1,
- Stéphane Audic1,
- Olivier Poirot1,
- Pascal Hingamp1,
- Virginie Seltzer1,
- Deborah Byrne1,
- Audrey Lartigue1,
- Magali Lescot1,
- Alain Bernadac2,
- Julie Poulain3,
- Chantal Abergel1,4 and
- Jean-Michel Claverie1,4
- 1 Structural & Genomic Information Laboratory (Centre National de la Recherche Scientifique, UPR2589), Mediterranean Institute of Microbiology (IFR88), Aix-Marseille University, Parc Scientifique de Luminy, FR-13288 Marseille, France;
- 2 Mediterranean Institute of Microbiology (IFR88), 13402 Marseille Cedex 20, France;
- 3 Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, FR-91057 Evry, France
Abstract
Mimivirus, a virus infecting Acanthamoeba, is the prototype of the Mimiviridae, the latest addition to the nucleocytoplasmic large DNA viruses. The Mimivirus genome encodes close to 1000 proteins, many of them never before encountered in a virus, such as four amino-acyl tRNA synthetases. To explore the physiology of this exceptional virus and identify the genes involved in the building of its characteristic intracytoplasmic “virion factory,” we coupled electron microscopy observations with the massively parallel pyrosequencing of the polyadenylated RNA fractions of Acanthamoeba castellanii cells at various time post-infection. We generated 633,346 reads, of which 322,904 correspond to Mimivirus transcripts. This first application of deep mRNA sequencing (454 Life Sciences [Roche] FLX) to a large DNA virus allowed the precise delineation of the 5′ and 3′ extremities of Mimivirus mRNAs and revealed 75 new transcripts including several noncoding RNAs. Mimivirus genes are expressed across a wide dynamic range, in a finely regulated manner broadly described by three main temporal classes: early, intermediate, and late. This RNA-seq study confirmed the AAAATTGA sequence as an early promoter element, as well as the presence of palindromes at most of the polyadenylation sites. It also revealed a new promoter element correlating with late gene expression, which is also prominent in Sputnik, the recently described Mimivirus “virophage.” These results—validated genome-wide by the hybridization of total RNA extracted from infected Acanthamoeba cells on a tiling array (Agilent)—will constitute the foundation on which to build subsequent functional studies of the Mimivirus/Acanthamoeba system.
Footnotes
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↵4 Corresponding authors.
E-mail Jean-Michel.Claverie{at}univmed.fr.
E-mail Chantal.Abergel{at}igs.cnrs-mrs.fr.
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[Supplemental material is available online at http://www.genome.org. The sequencing data from this study have been submitted to the NCBI Short Read Archive (http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi) under accession no. SRA010763. The microarray data from this study have been submitted to ArrayExpress (http://www.ebi.ac.uk/microarray-as/ae/) under accession nos. A-MEXP-1782 and E-MTAB-187.]
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Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.102582.109.
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- Received November 29, 2009.
- Accepted February 5, 2010.
Freely available online through the Genome Research Open Access option.
- Copyright © 2010 by Cold Spring Harbor Laboratory Press