PROGRAMMED CELL-DEATH BY HOK SOK OF PLASMID R1 - COUPLED NUCLEOTIDE COVARIATIONS REVEAL A PHYLOGENETICALLY CONSERVED FOLDING PATHWAY IN THEHOK FAMILY OF MESSENGER-RNAS/

The hok/sok system of plasmid R1 mediates plasmid maintenance by killi ng of plasmid-free cells. Translation of the stable toxin-encoding hok mRNA is repressed by the unstable Sok antisense RNA. Using genetic al gorithm simulations and phylogenetic comparisons, we analyse five plas mid-encoded and two chromosome-encoded hok-homologous mRNAs. A similar folding pathway was found for all mRNAs, Metastable hairpins at the v ery 5'-ends of the mRNAs were predicted to prevent the formation of st ructures required for translation and antisense RNA binding. Thus the folding of the mRNA 5'-ends appears to explain the apparent inactivity of the nascent transcripts. Ln the full-length mRNAs, long-range 5' t o 3' interactions were predicted in all cases. The 5' to 3' interactio ns lock the mRNAs in inactive configurations. Transition of the mRNAs is activated by 3' exonucleolytic processing. Simulation of the 3' pro cessing predicted that it triggers rearrangements of the mRNA 5'-ends with the formation of translational activator and antisense RNA target hairpins. Alignment of the mRNA sequences revealed a large number of nucleotide convariations that support the existence of the proposed se condary structures. Furthermore, coupled covariations support the fold ing pathway and provide evidence that the mRNA 5'-ends pair with three different partners during the proposed series of dynamic RNA rearrang ements. (C) 1997 Academic Press Limited.