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Maximum likelihood analysis of mammalian p53 indicates the presence of positively selected sites and higher tumorigenic mutations in purifying sites

Khan, M.M.G.; Ryden, A.M.; Chowdhury, M.S.; Hasan, M.A. and Kazi, Julhash U. LU (2011) In Gene 483(1-2). p.29-35
Abstract
The tumor suppressor gene TP53 (p53) maintains genome stability. Mutation or loss of p53 is found in most cancers. Analysis of evolutionary constrains and p53 mutations reveal important sites for concomitant functional studies. In this study, phylogenetic analyses of the coding sequences of p53 from 26 mammals were carried out by applying a maximum likelihood method. The results display two branches under adaptive evolution in mammals. Moreover, each codon of p53 was analyzed by the PAML method for presence of positively selected sites. PAML identified several statistically significant amino acids that undergo positive selection. The data indicates that amino acids responsible for the core functions of p53 are highly conserved, while... (More)
The tumor suppressor gene TP53 (p53) maintains genome stability. Mutation or loss of p53 is found in most cancers. Analysis of evolutionary constrains and p53 mutations reveal important sites for concomitant functional studies. In this study, phylogenetic analyses of the coding sequences of p53 from 26 mammals were carried out by applying a maximum likelihood method. The results display two branches under adaptive evolution in mammals. Moreover, each codon of p53 was analyzed by the PAML method for presence of positively selected sites. PAML identified several statistically significant amino acids that undergo positive selection. The data indicates that amino acids responsible for the core functions of p53 are highly conserved, while positively selected sites are predominantly located in the N- and C-terminus of p53. Further analysis of evolutionary pressure and mutations showed the occurrence of more frequent tumorigenic mutations in purifying sites of p53. (Less)
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author
publishing date
type
Contribution to journal
publication status
published
subject
keywords
p53, Phylogenetic analysis, Maximum likelihood
in
Gene
volume
483
issue
1-2
pages
29 - 35
publisher
Elsevier
external identifiers
  • scopus:79960250940
ISSN
1879-0038
DOI
10.1016/j.gene.2011.05.011
language
English
LU publication?
no
id
e60390d6-c8d3-44be-81d8-3c6acc867ef4 (old id 4250257)
date added to LUP
2014-02-13 17:08:52
date last changed
2017-07-30 04:20:51
@article{e60390d6-c8d3-44be-81d8-3c6acc867ef4,
  abstract     = {The tumor suppressor gene TP53 (p53) maintains genome stability. Mutation or loss of p53 is found in most cancers. Analysis of evolutionary constrains and p53 mutations reveal important sites for concomitant functional studies. In this study, phylogenetic analyses of the coding sequences of p53 from 26 mammals were carried out by applying a maximum likelihood method. The results display two branches under adaptive evolution in mammals. Moreover, each codon of p53 was analyzed by the PAML method for presence of positively selected sites. PAML identified several statistically significant amino acids that undergo positive selection. The data indicates that amino acids responsible for the core functions of p53 are highly conserved, while positively selected sites are predominantly located in the N- and C-terminus of p53. Further analysis of evolutionary pressure and mutations showed the occurrence of more frequent tumorigenic mutations in purifying sites of p53.},
  author       = {Khan, M.M.G. and Ryden, A.M. and Chowdhury, M.S. and Hasan, M.A. and Kazi, Julhash U.},
  issn         = {1879-0038},
  keyword      = {p53,Phylogenetic analysis,Maximum likelihood},
  language     = {eng},
  number       = {1-2},
  pages        = {29--35},
  publisher    = {Elsevier},
  series       = {Gene},
  title        = {Maximum likelihood analysis of mammalian p53 indicates the presence of positively selected sites and higher tumorigenic mutations in purifying sites},
  url          = {http://dx.doi.org/10.1016/j.gene.2011.05.011},
  volume       = {483},
  year         = {2011},
}