Book of Abstracts: Albany 2003
June 17-21 2003
Does Dinucleotide Composition of Herepes Viruses Reflect the Evolutionary Transitions?
Herpes viruses are known to cause chronic/latent/recurrent infections and hence are extensively studied. On basis of the biological characteristics like tissue tropism, host range, reproductive cycle and amino acid identities in protein sequences, this group of DNA viruses is classified into alpha, beta and gamma types (1). But does the phenotypic similarities in each subgroup, necessarily reflect the evolutionary relatedness? We have tried to address this question by analyzing the genomic composition of available herpes viral genome sequences (alpha: 10, beta: 7, gamma: 9, unclassified: 1, Total: 27) since each organism has characteristic genome composition and the relative abundances of dinucleotides are similar in similar organisms and different in distant organisms (2).
Using statistical techniques of multiple analysis of variance (MANOVA) and principle component analysis (PCA) we could classify the viruses into groups of similar dinucleotide composition. The dinucleotide composition of whole genome sequences as well as for open reading frames and intergenic regions were analyzed. Our analysis shows that the viruses belonging to the same subgroup have similar dinucleotide composition. Exception to this was that of Macaca Mulatta rhadinovisus and Human herpesvirus 8. Both the viruses are biologically classified into the gamma subgroup. But these two viruses are a little distant from other members of their biological subgroup in terms of the dinucleotide composition. Thus, these two viruses have phenotypic characteristics similar to the gamma viruses but in terms of genomic composition they are distant from this subgroup. This suggests a possibility that these two viruses may be undergoing evolutionary transition, which is reflected in their DNA composition but not yet seen in their phenotypic characteristics.
The similar dinucleotide compositions in similar organisms may be due to the DNA structural constraints. We carried out DNA structure prediction and analysis of these genome sequences. The study showed that similar viruses have similar fraction of bent DNA, especially the gamma viruses. This analysis further confirmed the different nature of Macaca Mulatta rhadinovisus and Human herpesvirus 8, which have a lower fraction of bent DNA compared to other gamma viruses.
1Molecular Biophysics Unit