Using the Genome Sequencer FLX System from 454 Life Sciences, a Roche Company, the researchers performed the first ever viral transcriptome analysis by deep sequencing RNAs expressed by infected amoebas throughout the Mimivirus replication cycle (1). Unexpectedly, the analysis revealed 75 new genes, including 26 producing non-coding RNAs. The existence, and so far unknown function, of these additional genes in the already plethoric Mimivirus genome could radically change the current understanding of the way large viruses operate.
Since the discovery and deciphering of its genome in 2004, the giant Mimivirus has blurred the traditional boundaries between viruses and cellular organisms, spurring debate between virologists and evolutionary biologists. In a quest to fully characterize the Mimivirus transcriptome and obtain new insights into its gene and protein functions, the researchers turned to the Genome Sequencer FLX System. “Not only were we able to confirm the 910 previously predicted protein-coding genes, but we also identified 75 novel genes in the Mimivirus,” explained Jean-Michele Claverie and Chantal Abergel, senior authors of the study. “The long reads generated by the GS FLX System were critical for the assembly of full length transcripts, identification of polycistronic mRNA and for the discovery of short transcripts, since the 5’ and 3’ tags were contained within a single read.”
Sequence mapping also allowed the precise delineation of most promoter regions and the identification of the sequence motif governing the early versus late expression of Mimivirus genes. Excitingly, the study revealed a new promoter element correlating with late gene expression that is also prominent in Sputnik, the recently described Mimivirus “virophage”.
Moving forward, the researchers plan to perform similar viral transcriptome analysis in the presence and absence of various inhibitors, and with other amoeba strains that have different sensitivity to the Mimivirus. Since recent metagenomics studies suggest that Mimivirus could be the prototype of numerous marine viruses infecting a variety of planktonic micro-organisms, a specific program is devoted search for the Mimivirus’ marine relatives in the ongoing international TARA-Oceans expedition.
“We are pleased to see continued widespread adoption of 454 Sequencing systems in virology research,” said Ulrich Schwoerer, Head of Global Marketing at 454 Life Sciences. “This particular study demonstrates, for the first time, the unique capabilities of the technology for comprehensive transcriptome analysis of viral genomes. We are excited to follow the team’s continued work in this field.”