Divergent evolution may link human immunodeficiency virus GP41 to human CD4

The role of the genetic code in generating new coding sequences inside existing genes

The genetic code has a very interesting property--it generates an open reading frame (ORF) inside a coding sequence, in a specific phase of the antisense strand with much higher probability than in the random DNA sequences. Furthermore, these antisense ORFs (A-ORFs) possess the same features as real genes--the asymmetry in the nucleotide composition at the first and second positions in codons. About two thirds of the 2997 overlapping ORFs in the yeast genome possess this feature. Thus, the question arises: has this feature of the genetic code been exploited in the evolution of genes? We have searched the FASTA data bases for homologies with the antisense translation products of a specific class of genes and we have found some sequences with relatively high homology. Many of them have scores which could be randomly found in the searched data bases with a probability lower than 10(-6). We conclude that some genes could arise by positioning a copy of the original gene under a promoter in the opposite direction in such a way that both, the original gene and its copy initially use the same nucleotides in the third, degenerated positions in codons.

Selenium and cellular immunity. Evidence that selenoproteins may be encoded in the +1 reading frame overlapping the human CD4, CD8, and HLA-DR genes

Selenium deficiency can lead to impaired immune function and reduced T-cell counts, as well as various specific disorders. Significantly, in ARC and AIDS patients, a progressive decline in plasma Se, paralleling T-cell loss, has been widely documented. Since evidence now suggests that there is an extremely high turnover of CD4+ T-cells in AIDS patients, with billions of new cells lost and replaced daily, any exceptional requirement for Se in lymphocytes could contribute to this progressive Se depletion. Thus, it may be significant that, overlapping the known genes in the +1 reading frame, the mRNAs of several T-cell associated genes (CD4, CD8, HLA-DR p33) have open reading frames (ORFs) with as many as 10 in-frame UGA codons (CD4, p33), a clustering that is highly improbable by chance alone, and reminiscent of selenoprotein P, the predominant plasma form of Se. The presence of these ORFs, along with potential stem-loop RNA structures displaying consensus selenocysteine insertion sequences, AUG(N)mAAA(N)nUGR, suggests that these mRNAs may encode selenoproteins, in addition to the known T-cell glycoproteins. If so, the roles of Se in the immune system may be more diverse than previously suspected.

Investigating hypothetical products from noncoding frames (HyPNoFs)

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.