title: Investigating hypothetical products from noncoding frames (HyPNoFs).
abstract: Hypothetical Products from Noncoding Frames (i.e., HyPNoFs) are hypothetical, not-coded proteins, translated from alternate reading frames (i.e., coding + 1 and coding + 2) of cDNAs. HyPNoFs of CD4, PKC, oncostatin, bcl-2 proto-oncogene, tumor suppressor p53, cystic fibrosis transmembrane regulator (CFTR), and tumor necrosis factors alpha and beta were searched as query sequences vs the SWISS-PROT data bank. Homology searchers carried out revealed that hypothetical products (i.e., HyPNoFs) may share high similarity with real protein products actually coded. Sequence similarity of hypothetical products to real proteins is sometimes very high, suggesting common conformational features, according to the Sander and Schneider cutoff value. This finding supports the hypothesis that eukaryotic DNA, currently considered to be monocistronic, might occasionally have polycistronic regions, carrying different protein messages on overlapping frames. As yet, polycistronic genes have been observed in viral genomes only. The presence of polycistronic regions in eukaryotic genes is likely reminiscent of an ancient strategy, rather than a present feature of the genome in eukaryotes. These data suggest that thorough investigation of HyPNoFs is likely to improve our ability to trace genes' evolution and to investigate structure-function relationships of protein and DNA sequences.
authors.affiliation: Raggio Italgene S.p.A., Pomezia, Roma, Italy.
authors.forename: A
authors.initials: A
authors.lastname: Facchiano
mesh_terms: D000595:Amino Acid Sequence; D015704:CD4 Antigens / Q000235:genetics; D019005:Cystic Fibrosis Transmembrane Conductance Regulator; D015870:Gene Expression; D006801:Humans; D008233:Lymphotoxin-alpha / Q000235:genetics; D008565:Membrane Proteins / Q000235:genetics; D008969:Molecular Sequence Data; D053683:Oncostatin M; D010455:Peptides / Q000235:genetics; D011493:Protein Kinase C / Q000235:genetics; D000090063:Proto-Oncogene Mas; D011518:Proto-Oncogene Proteins / Q000235:genetics; D019253:Proto-Oncogene Proteins c-bcl-2; D016364:Reading Frames / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D014409:Tumor Necrosis Factor-alpha / Q000235:genetics; D016159:Tumor Suppressor Protein p53 / Q000235:genetics
chemical_list: D015704:CD4 Antigens; C505032:CFTR protein, human; D008233:Lymphotoxin-alpha; C000715470:MAS1 protein, human; D008565:Membrane Proteins; C508351:OSM protein, human; D010455:Peptides; D000090063:Proto-Oncogene Mas; D011518:Proto-Oncogene Proteins; D019253:Proto-Oncogene Proteins c-bcl-2; D014409:Tumor Necrosis Factor-alpha; D016159:Tumor Suppressor Protein p53; D053683:Oncostatin M; D019005:Cystic Fibrosis Transmembrane Conductance Regulator; D011493:Protein Kinase C