Our goal was to identify evolutionary conserved frame transitions in protein 
coding regions and to uncover an underlying functional role of these structural 
aberrations. We used the ab initio frameshift prediction program, GeneTack, to 
detect reading frame transitions in 206 991 genes (fs-genes) from 1106 complete 
prokaryotic genomes. We grouped 102 731 fs-genes into 19 430 clusters based on 
sequence similarity between protein products (fs-proteins) as well as 
conservation of predicted position of the frameshift and its direction. We 
identified 4010 pseudogene clusters and 146 clusters of fs-genes apparently 
using recoding (local deviation from using standard genetic code) due to 
possessing specific sequence motifs near frameshift positions. Particularly 
interesting was finding of a novel type of organization of the dnaX gene, where 
recoding is required for synthesis of the longer subunit, τ. We selected 20 
clusters of predicted recoding candidates and designed a series of genetic 
constructs with a reporter gene or affinity tag whose expression would require a 
frameshift event. Expression of the constructs in Escherichia coli demonstrated 
enrichment of the set of candidates with sequences that trigger genuine 
programmed ribosomal frameshifting; we have experimentally confirmed four new 
families of programmed frameshifts.