Mutation hotspots in the p53 gene in tumors of different origin: correlation with evolutionary conservation and signs of positive selection.
We present a classification analysis of the mutation spectra of the p53 gene and construct maps of hotspots for the germline (Li-Fraumein syndrome), different types of tumors and their derived cell lines. While spectra from solid tumors share common hotspots with the germline spectrum, they also contain unique sets of somatic hotspots that are not observed in the germline. All these hotspots correspond to amino acid replacements in the DNA-binding interface of p53. The mutation spectra of lymphomas and cell lines derived from lymphomas and lung cancers contained few hotspots compared to solid tumors. Thus, the distribution of hotspots in the p53 gene appears to depend on the tumor type and cell growth conditions; this specificity is missed by the bulk hotspot analysis. A negative correlation was detected between the amino acid replacement propensity in tumors and evolutionary variability: the hotspots are located in the positions that are highly conserved in p53 and its paralogs, p63 and p73. In all the mutation spectra, substitutions leading to amino acid replacements strongly dominate over silent substitutions, indicating that functional sites evolving under strong purifying selection are subject to intensive positive selection in p53-dependent tumors. These results are compatible with the gain-of-function concept of the role of p53 in tumorigenesis.
Glazko
Galina V
GV
Stowers Institute for Medical Research, Kansas City, MO 64110, USA. gvg@Stowers-Institute.org
Koonin
Eugene V
EV
Rogozin
Igor B
IB
D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D018899:CpG Islands; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D016147:Genes, Tumor Suppressor; D016158:Genes, p53 / Q000235:genetics / Q000502:physiology*; D018095:Germ-Line Mutation; D006801:Humans; D008969:Molecular Sequence Data; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D009687:Nuclear Proteins / Q000737:chemistry / Q000235:genetics; D010750:Phosphoproteins / Q000737:chemistry / Q000235:genetics; D010802:Phylogeny; D012641:Selection, Genetic; D016415:Sequence Alignment; D013223:Statistics as Topic; D015534:Trans-Activators / Q000737:chemistry / Q000235:genetics; D014157:Transcription Factors; D000072160:Tumor Protein p73; D016159:Tumor Suppressor Protein p53 / Q000737:chemistry / Q000235:genetics; D025521:Tumor Suppressor Proteins
D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; D010750:Phosphoproteins; C115051:TP63 protein, human; C000606460:TP73 protein, human; D015534:Trans-Activators; D014157:Transcription Factors; D000072160:Tumor Protein p73; D016159:Tumor Suppressor Protein p53; D025521:Tumor Suppressor Proteins