Cloning and characterization of extended hammerheads from a diverse set of caudate amphibians.

Satellite 2 (sat2) elements from six species representing four caudate amphibian families were cloned and analyzed. Despite differences in the abundance of this element, the tandemly repeated genomic organization found for sat2 in earlier investigations was conserved in the newly investigated species. The ability of sat2 transcripts to catalyze their own site-specific self-cleavage using an extended hammerhead (HH) motif had also been conserved. This motif is similar to the HH found in a number of infectious plant RNAs, but has an abbreviated stem III region and an internally looped stem I extension that distinguish it from the prototypical HH. The extended HH analyzed in this survey can be further organized into two groups on the basis of shared sequences and structural details in the peripheral stem-loop structures. HH derived from the family Salamandridae constitute one group, whereas HH from all other salamanders that have been investigated belong to the other group. Although many of the natural variants did not cleave efficiently in vitro, examples of relatively active variants for each design were found. This survey has therefore identified two designs that are suitable starting models for the structural and functional analysis of the extended HH.