Genome 3'-end repair in dengue virus type 2

Genomes of RNA viruses encounter a continual threat from host cellular ribonucleases. Therefore, viruses have evolved mechanisms to protect the integrity of their genomes. To study the mechanism of 3′-end repair in dengue virus-2 in mammalian cells, a series of 3′-end deletions in the genome were evaluated for virus replication by detection of viral antigen NS1 and by sequence analysis. Limited deletions did not cause any delay in the detection of NS1 within 5 d. However, deletions of 7–10 nucleotides caused a delay of 9 d in the detection of NS1. Sequence analysis of RNAs from recovered viruses showed that at early times, virus progenies evolved through RNA molecules of heterogeneous lengths and nucleotide sequences at the 3′ end, suggesting a possible role for terminal nucleotidyl transferase activity of the viral polymerase (NS5). However, this diversity gradually diminished and consensus sequences emerged. Template activities of 3′-end mutants in the synthesis of negative-strand RNA in vitro by purified NS5 correlate well with the abilities of mutant RNAs to repair and produce virus progenies. Using the Mfold program for RNA structure prediction, we show that if the 3′ stem–loop (3′ SL) structure was abrogated by mutations, viruses eventually restored the 3′ SL structure. Taken together, these results favor a two-step repair process: non-template-based nucleotide addition followed by evolutionary selection of 3′-end sequences based on the best-fit RNA structure that can support viral replication.     

Stability and evolution of overlapping genes

Abstract.— When the same sequence of nucleotides codes for regions of more than one functional polypeptide, this sequence contains overlapping genes. Overlap is most common in rapidly evolving genomes with high mutation rates such as viruses, bacteria, and mitochondria. Overlap is thought to be important as: (1) a means of compressing a maximum amount of information into short sequences of structural genes; and (2) as a mechanism for regulating gene expression through translational coupling of functionally related polypeptides. The stability of overlapping codes is examined in relation to the information cost of overlap and the mutation rate of the genome. The degree of overlap in a given population will tend to become monomorphic. Evolution toward partial overlap of genes is shown to depend on a convex cost function of overlap. Overlap does not evolve when expression of overlapping genes is mutually exclusive and produced by rare mutations to the wild-type genome. Assuming overlap increases coupling between functionally related genes, the conditions favoring overlap are explored in relation to the kinetics of gene activation and decay. Coupling is most effective for genes in which the gene overlapping at its 5'end (leading gene) decays rapidly, while the gene overlapping at the 3'end (induced gene) decays slowly. If gene expression can feedback on itself (autocatalysis), then high rates of activation favor overlap.     

The evolution of meiosis and sexual reproduction

It has been argued that because intermediate states would not be advantageous, it is impossible for natural selection to account for the evolution of meiosis and sexual reproduction. The argument is invalid because a reasonable hypothesis is presented. The hypothesis is developed from a consideration of unicellular eukaryotes and prokaryotes and is that the ancestral eukaryote had a form of parasexual cycle with 'somatic' or 'mitotic' recombination. Later mitosis, then meiosis evolved. In multicellular organisms genetic recombination then usually became restricted to meiosis. Several predictions are made that could be tested in the near future. A conclusion is that we have been misled by treating meiosis and genetic recombination as more or less synonomous. The question of the ultimate origin of recombination is more obscure but it is pointed out that recombination could give the most immediate advantage early in the origin of life, particularly with a hypercycle model. It could result in the combination of advantageous quasi-species (short nucleotidc sequences) into one genome, and it could eliminate ineffective combinations. There are discussions of the scientific role of hypotheses for the origin of complex biological features and on the biological success of cooperative units of DNA.