mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus
| Autor: | Matthieu Legendre, Alain Bernadac, Pascal Hingamp, Chantal Abergel, Stéphane Audic, Olivier Poirot, Julie Poulain, Audrey Lartigue, Magali Lescot, Deborah Byrne, Jean-Michel Claverie, Virginie Seltzer |
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| Přispěvatelé: | Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie structurale et microbiologie (IBSM), Université de la Méditerranée - Aix-Marseille 2-Université Paul Cézanne - Aix-Marseille 3-Université de Provence - Aix-Marseille 1-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), ANR-08-BLAN-0089,MIMIVIRUS,Etude de la relation hôte pathogène du système Acanthamoeba/Mimivirus(2008) |
| Rok vydání: | 2010 |
| Předmět: |
Gene Expression Regulation
Viral DNA Complementary Genes Viral [SDV]Life Sciences [q-bio] Acanthamoeba Genome Viral Nucleocytoplasmic large DNA viruses Viral Proteins Genetics Animals Mimiviridae Giant Virus RNA Messenger Genetics (clinical) Mimivirus biology Pandoravirus Gene Expression Profiling Research Virophage Virion Sequence Analysis DNA biology.organism_classification Microscopy Electron MRNA Sequencing RNA Viral Megavirus |
| Zdroj: | Genome Research Genome Research, 2010, 20 (5), pp.664-674. ⟨10.1101/gr.102582.109⟩ |
| ISSN: | 1088-9051 1549-5469 |
| DOI: | 10.1101/gr.102582.109 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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