Phylogenetic analysis and predicted functional effect of protein mutations of E6 and E7 HPV16 strains isolated in Indonesia
Abstract: E6 and E7 are
oncoproteins of HPV16. Natural amino acid variation in HPV16 E6 can alter its
carcinogenic potential. The aim of this study was to analyze phylogenetically
E6 and E7 genes and proteins of HPV16 from Indonesia and predict the effects of
single amino acid substitution on protein function. This analysis could be used
to reduce time, effort, and research cost as initial screening in selection of
protein or isolates to be tested in vitro or in vivo.
Methods: In this study, E6 and E7 gene sequences were obtained from 12
samples of Indonesian isolates,
which were compared with HPV16R
(prototype) and 6 standard isolates in the category of European (E), Asian
(As), Asian-American (AA), African-1 (Af-1), African-2 (Af-2), and North
American (NA) branch from Genbank. Bioedit v.7.0.0 was used to analyze the
composition and substitution of single amino acids. Phylogenetic analysis of E6
and E7 genes and proteins was performed using Clustal X (1.81) and NJPLOT
softwares. Effects of single amino acid substitutions on protein function of E6
and E7 were analysed by SNAP.
Results: Java variants and isolate ui66* belonged to European branch,
while the others belonged to Asian and African branches. Twelve changes of
amino acids were found in E6 and one in E7 proteins. SNAP analysis showed two
non neutral mutations, i.e. R10I and C63G in E6 proteins. R10I mutations were
found in Af-2 genotype (AF472509) and Indonesian isolates (Af2*), while C63G
mutation was found only in Af2*.
Conclusion: E6 proteins of HPV16 variants were more variable than E7.
SNAP analysis showed that only E6 protein of African-2 branch had functional
differences compared to HPV16R.
Author: Dwi Wulandari,
Lisnawati Rachmadi, Tjahjani M. Sudiro
Journal Code: jpkedokterangg150329