Although mitochondria derive from alpha-proteobacteria, many proteins acting in 
this organelle did not originate from bacteria. In particular, phylogenetic 
evidence indicates that RNA polymerase, DNA polymerase and DNA primase--with 
homologues encoded by T3/T7-like bacteriophages--have replaced the ancestral 
proteins of bacterial origin. To date, there was no clear explanation for this 
puzzling observation. Bacterial genomics has now revealed the presence of 
cryptic prophages that are related to T3/T7 in several genomes of 
proteobacteria. We propose that such a prophage was present in the ancestral 
alpha-proteobacterium at the origin of mitochondria and that RNA polymerase, DNA 
polymerase and DNA primase encoded by this prophage replaced the original 
bacterial enzymes to function in mitochondria. Another T3/T7 viral-like RNA 
polymerase is functional in the chloroplast, indicating that a strong selection 
pressure has favored replacement of some cellular proteins by viral proteins in 
organelle evolution.