Different papillomaviruses have different repertoires of transcription factor binding sites: convergence and divergence in the upstream regulatory region

BMC Evolutionary Biology
Santiago García-VallvéIgnacio G Bravo

Abstract

Papillomaviruses (PVs) infect stratified squamous epithelia in warm-blooded vertebrates and have undergone a complex evolutionary process. The control of the expression of the early ORFs in PVs depends on the binding of cellular and viral transcription factors to the upstream regulatory region (URR) of the virus. It is believed that there is a core of transcription factor binding sites (TFBS) common to all PVs, with additional individual differences, although most of the available information focuses only on a handful of viruses. We have studied the URR of sixty-one PVs, covering twenty different hosts. We have predicted the TFBS present in the URR and analysed these results by principal component analysis and genetic algorithms. The number and nature of TFBS in the URR might be much broader than thus far described, and different PVs have different repertoires of TFBS. There are common fingerprints in the URR in PVs that infect primates, although the ancestors of these viruses diverged a long time ago. Additionally, there are obvious differences between the URR of alpha and beta PVs, despite these PVs infect similar histological cell types in the same host, i.e. human. A thorough analysis of the TFBS in the URR might provide cr...Continue Reading

References

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Jun 1, 2005·Trends in Genetics : TIG·Joseph W Thornton, Bryan Kolaczkowski
Sep 27, 2005·Trends in Microbiology·Santiago García-VallvéIgnacio G Bravo

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Citations

Aug 24, 2006·Virus Genes·Ignacio G Bravo, Angel Alonso
Sep 18, 2008·Biology Direct·Pere PuigbòSantiago Garcia-Vallve
Jan 31, 2015·Evolution, Medicine, and Public Health·Ignacio G Bravo, Marta Félez-Sánchez
May 11, 2010·Journal of Veterinary Diagnostic Investigation : Official Publication of the American Association of Veterinary Laboratory Diagnosticians, Inc·Cristina M WeinerSue Vandewoude
Jul 6, 2017·Viruses·Imelda Martínez-RamírezMarcela Lizano
Aug 27, 2010·Trends in Microbiology·Ignacio G BravoMarc Gottschling

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Methods Mentioned

BETA
PCA

Software Mentioned

PROTPARS
MATCH
NEUROSHELLL
CLUSTALW
SEQBOOT
CONSENSE
DIALIGN
DNAPARS
PHYLIP
DNADIST

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