Mimivirus gene promoters exhibit an unprecedented conservation among all eukaryotes - PubMed (original) (raw)

Comparative Study

. 2005 Oct 11;102(41):14689-93.

doi: 10.1073/pnas.0506465102. Epub 2005 Oct 3.

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Comparative Study

Mimivirus gene promoters exhibit an unprecedented conservation among all eukaryotes

Karsten Suhre et al. Proc Natl Acad Sci U S A. 2005.

Abstract

The initial analysis of the recently sequenced genome of Acanthamoeba polyphaga Mimivirus, the largest known double-stranded DNA virus, predicted a proteome of size and complexity more akin to small parasitic bacteria than to other nucleocytoplasmic large DNA viruses and identified numerous functions never before described in a virus. It has been proposed that the Mimivirus lineage could have emerged before the individualization of cellular organisms from the three domains of life. An exhaustive in silico analysis of the noncoding moiety of all known viral genomes now uncovers the unprecedented perfect conservation of an AAAATTGA motif in close to 50% of the Mimivirus genes. This motif preferentially occurs in genes transcribed from the predicted leading strand and is associated with functions required early in the viral infectious cycle, such as transcription and protein translation. A comparison with the known promoter of unicellular eukaryotes, amoebal protists in particular, strongly suggests that the AAAATTGA motif is the structural equivalent of the TATA box core promoter element. This element is specific to the Mimivirus lineage and may correspond to an ancestral promoter structure predating the radiation of the eukaryotic kingdoms. This unprecedented conservation of core promoter regions is another exceptional feature of Mimivirus that again raises the question of its evolutionary origin.

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Figures

Fig. 1.

Fig. 1.

The distribution of the position of the AAAATTGA motif with respect to the predicted gene start shows the location of the conserved element at ≈50–110 nt.

Fig. 2.

Fig. 2.

The sequence logo shows the conserved AT-rich neighborhood of the exactly conserved AAAATTGA octamer. The logo was based on 400 genes with a strictly conserved AAAATTGA motif; 3 genes with a motif that is <20 nt from the predicted translation start were not included in the computation of the logo. (See Fig. 5 for the corresponding logo of the

meme

motif.)

Fig. 3.

Fig. 3.

No relationship between the presence/absence of the AAAATTGA motif and the distance between two genes can be identified in the size distribution of Mimivirus intergenic regions. The exception is the virtual absence of the motif in intergenic regions that are too short to host it.

Fig. 4.

Fig. 4.

The alignment of the intergenic region of the paralogous gene cluster L175–L185 shows the perfect conservation of the AAAATTGA motif within intergenic regions that have otherwise more extensively diverged. Note that the AAAATTGA motif is part of the C terminus of gene L185 (indicated by white Xs).

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